[{"id":4400,"date":"2025-10-03T15:17:52","date_gmt":"2025-10-03T15:17:52","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4400"},"modified":"2025-10-03T15:17:54","modified_gmt":"2025-10-03T15:17:54","slug":"deepof","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/deepof\/","title":{"rendered":"DeepOF"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

Lucas Miranda and colleagues at the Max Planck Institute of Psychiatry have developed DeepOF <\/strong>(Deep Open Field), a powerful open-source software package designed to process pose estimation data acquired using tools like DeepLabCut or SLEAP. DeepOF’s transforms raw video footage into structured time-series data of tracked body parts, enabling sophisticated post-hoc analysis, embedding of motion tracking data, and automated behavior annotation.<\/p>\n

A major strength of DeepOF is its comprehensive approach to annotating and interpreting behavioral patterns, offering both established and novel methods:<\/p>\n

Supervised Pipeline:<\/strong> This method uses rule-based annotators and pre-trained machine learning classifiers to reliably detect and measure predefined behavioral motifs (patterns you already know you’re looking for).<\/p>\n

Unsupervised Pipeline:<\/strong> This advanced feature uses deep clustering models to automatically extract and identify novel behavioral motifs without any prior definition.<\/p>\n

DeepOF is one of the first software packages to seamlessly integrate both supervised and unsupervised annotation pipelines. To help researchers understand the results from the unsupervised clusters, the software includes an interpretability pipeline using SHAP (SHapley Additive exPlanations) to explore the behavioral meaning of the extracted motifs.<\/p>\n

This accessible and robust software is available for download on the lab’s GitHub, along with links to the required DeepLabCut and SLEAP software.<\/p>\n

Thanks to Ellie Blumer for writing this post. She is a second-year neuroscience major and computer science minor at American University. She will be assisting with website content this year.<\/em><\/i><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the files!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/mlfpm\/deepof” link_option_url_new_window=”on”]<\/p>\n

All files are available in a GitHub repository.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/joss.theoj.org\/papers\/10.21105\/joss.05394″ link_option_url_new_window=”on”]Find out more in the authors’ publication![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

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[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] Lucas Miranda and colleagues at the Max Planck Institute of Psychiatry have developed DeepOF (Deep Open Field), a powerful open-source software package designed to process pose […]<\/p>\n","protected":false},"author":2065,"featured_media":4399,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[153,167,168,169,156],"project_tag":[2372,2022,2243,2263,2406],"class_list":["post-4400","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-measurement","project_category-data-analysis-software","project_category-video-analysis-data-analysis","project_category-behavior-analysis","project_category-freely-moving","project_tag-analysis-pipeline","project_tag-deep-lab-cut","project_tag-pose-estimation","project_tag-sleap","project_tag-video-analysis"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4400","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/2065"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4400"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4400\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4399"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4400"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4400"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4400"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4379,"date":"2025-06-27T13:38:44","date_gmt":"2025-06-27T13:38:44","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4379"},"modified":"2025-06-27T13:38:46","modified_gmt":"2025-06-27T13:38:46","slug":"active-commutator","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/active-commutator\/","title":{"rendered":"Active Commutator"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”0em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/06\/wiring_diagram-1.png” _builder_version=”3.26.3″ transform_scale=”131%|131%” max_width=”40%” module_alignment=”center” transform_translate=”78px|19px” transform_origin=”124%|66%”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”372px” custom_padding=”2em|0|0px|0||” link_option_url_new_window=”on”]<\/p>\n

<\/span><\/p>\n

<\/span><\/p>\n

Thomas Akam, from the University of Oxford<\/a>, has developed an open-source active commutator designed to simplify one critical challenge of electrophysiology. This device addresses the common issue of tether tangling during experiments with freely moving subjects. The commutator relies on a Hall-Effect sensor detecting the rotation of the cable, this information is continuously fed to an Adafruit microcontroller that operates a servo motor to counter-rotate the cable as needed, preventing twisting and ensuring clear, uninterrupted data collection. The system can also be paused, restarted, and its neutral position recalibrated with simple button presses, allowing for flexible operation. This accessible tool provides a robust solution for maintaining tether integrity in dynamic experimental setups, making electrophysiology more efficient for labs to replicate and adapt.\u00a0<\/span><\/p>\n

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications.\u00a0<\/i><\/span>RRID:SCR_027098<\/i><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-423px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|22px|5px|0px|false|false” custom_margin=”|-7px||397px||” _builder_version=”3.26.3″ width=”74.2%” min_height=”251.5px” locked=”off”][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the files!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ width=”100%” custom_padding=”5px|5px|5px|92px|false|false” link_option_url=”https:\/\/github.com\/ThomasAkam\/active_commutator” link_option_url_new_window=”on”]<\/p>\n

All files are available in a GitHub repository.<\/p>\n

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[\/et_pb_text][et_pb_divider color=”#ffffff” divider_position=”center” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_portfolio fullwidth=”off” posts_number=”4″ include_categories=”173″ show_categories=”off” zoom_icon_color=”rgba(0,0,0,0)” hover_overlay_color=”rgba(0,0,0,0)” _builder_version=”3.26.3″ title_level=”h6″ background_color=”#121212″ text_orientation=”left” locked=”off”][\/et_pb_portfolio][\/et_pb_column][et_pb_column type=”2_5″ _builder_version=”3.26.3″][et_pb_contact_form captcha=”off” email=”openbehavior@gmail.com” title=”Have questions? Send us an email!” success_message=”Thanks! We’ll try and get back to you soon!” _builder_version=”3.26.3″ title_level=”h3″ title_font=”|600|||||||” title_text_align=”center” title_font_size=”19px” captcha_text_color=”#ffffff” captcha_font_size=”46px” custom_button=”on” button_text_size=”13px” button_text_color=”#ffffff” button_bg_color=”#000000″ text_orientation=”left” custom_margin=”20px||10px||false|false” custom_padding=”5px|5px|5px|5px|false|false”][et_pb_contact_field field_id=”Name” field_title=”Name” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Email” field_title=”Email Address” field_type=”email” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Message” field_title=”Message” field_type=”text” fullwidth_field=”on” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][\/et_pb_contact_form][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”0em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/06\/wiring_diagram-1.png” _builder_version=”3.26.3″ transform_scale=”131%|131%” max_width=”40%” module_alignment=”center” transform_translate=”78px|19px” transform_origin=”124%|66%”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”372px” custom_padding=”2em|0|0px|0||” link_option_url_new_window=”on”] Thomas Akam, from the University of Oxford, has developed an open-source active commutator designed to simplify one critical challenge of electrophysiology. This device […]<\/p>\n","protected":false},"author":4165,"featured_media":4369,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[153,148,150,156],"project_tag":[2240,2416,2195,761],"class_list":["post-4379","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-measurement","project_category-neural-recording","project_category-electrical-recording","project_category-freely-moving","project_tag-commutator","project_tag-ephys","project_tag-operant-behavior","project_tag-rodent"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4379","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/4165"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4379"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4379\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4369"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4379"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4379"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4379"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4351,"date":"2025-05-21T15:31:22","date_gmt":"2025-05-21T15:31:22","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4351"},"modified":"2025-05-21T15:32:41","modified_gmt":"2025-05-21T15:32:41","slug":"an-implant-for-diaphragm-emg-recordings-in-awake-rats","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/an-implant-for-diaphragm-emg-recordings-in-awake-rats\/","title":{"rendered":"Implant for Reliable Diaphragm EMG Recordings in Awake, Behaving Rats"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/05\/Screenshot-2025-05-21-at-11.11.05\u202fAM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

Breathing is a neuromuscular process that has been historically difficult to study in animal models. Typically, electromyography (EMG) or other approaches to record from respiratory muscles are conducted while the subject is under anesthesia, which limits our understanding of these processes during awake states. To address this limitation, Taylor Holmes and Jesus Penaloza-Aponte, and colleagues from the University of Florida<\/a> and Marquette University<\/a>, have developed a chronic implant for EMG recordings in the diaphragm of freely behaving rats. The implant is low cost and takes only 1 hour to build, and the group has demonstrated the success and reliability of these implants in publications (Malone et al., 2022<\/a>; Holmes et al., 2024<\/a>). Their recent eNeuro publication provides full documentation on how to build and use these implants in your own research.<\/p>\n

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications.\u00a0<\/i><\/span>RRID:SCR_026968<\/i><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.eneuro.org\/content\/12\/2\/ENEURO.0444-24.2025″ link_option_url_new_window=”on”]For documentation on how to build and use these implants, check out the eNeuro publication![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

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[\/et_pb_text][et_pb_divider color=”#ffffff” divider_position=”center” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_portfolio fullwidth=”off” posts_number=”4″ include_categories=”173″ show_categories=”off” zoom_icon_color=”rgba(0,0,0,0)” hover_overlay_color=”rgba(0,0,0,0)” _builder_version=”3.26.3″ title_level=”h6″ background_color=”#121212″ text_orientation=”left” locked=”off”][\/et_pb_portfolio][\/et_pb_column][et_pb_column type=”2_5″ _builder_version=”3.26.3″][et_pb_contact_form captcha=”off” email=”openbehavior@gmail.com” title=”Have questions? Send us an email!” success_message=”Thanks! We’ll try and get back to you soon!” _builder_version=”3.26.3″ title_level=”h3″ title_font=”|600|||||||” title_text_align=”center” title_font_size=”19px” captcha_text_color=”#ffffff” captcha_font_size=”46px” custom_button=”on” button_text_size=”13px” button_text_color=”#ffffff” button_bg_color=”#000000″ text_orientation=”left” custom_margin=”20px||10px||false|false” custom_padding=”5px|5px|5px|5px|false|false”][et_pb_contact_field field_id=”Name” field_title=”Name” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Email” field_title=”Email Address” field_type=”email” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Message” field_title=”Message” field_type=”text” fullwidth_field=”on” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][\/et_pb_contact_form][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/05\/Screenshot-2025-05-21-at-11.11.05\u202fAM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] Breathing is a neuromuscular process that has been historically difficult to study in animal models. Typically, electromyography (EMG) or other approaches to record from respiratory muscles […]<\/p>\n","protected":false},"author":3703,"featured_media":4352,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[153,156],"project_tag":[2419,791,2354,807,760,2420],"class_list":["post-4351","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-measurement","project_category-freely-moving","project_tag-breathing","project_tag-chronic-recording","project_tag-emg","project_tag-hardware","project_tag-rat","project_tag-respiration"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4351","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/3703"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4351"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4351\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4352"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4351"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4351"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4351"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4337,"date":"2025-05-08T16:05:37","date_gmt":"2025-05-08T16:05:37","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4337"},"modified":"2025-05-09T14:33:17","modified_gmt":"2025-05-09T14:33:17","slug":"bell-jar","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/bell-jar\/","title":{"rendered":"Bell Jar"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/05\/Screenshot-2025-05-08-at-11.54.54\u202fAM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

With the increase in high resolution imaging for histological analyses, Alec Soronow and colleagues from the Kim Neuroscience Lab<\/a> at UC Santa Cruz have developed Bell Jar, a semiautomated approach for histological analyses for mouse brain tissue. It is easily installable desktop software with tools written in Python, and is user-friendly for researchers without any computational background. It aligns tissue sections based on anatomical structures to a reference atlas (Allen Brain CCF) and offers various tools related to alignment, detection, and counting, due to its ability to detect fluorescent markers. It is also capable of high precision even when tissue is damaged. Bell Jar offers a solution to streamline processing large data sets, with only minor tuning needed from users.<\/p>\n

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications.\u00a0<\/i><\/span>RRID:SCR_026912<\/i><\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the files!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/asoronow\/belljar\/tree\/main” link_option_url_new_window=”on”]<\/p>\n

All software files are available in a GitHub repository.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.eneuro.org\/content\/12\/2\/ENEURO.0036-23.2025″ link_option_url_new_window=”on”]Find out more in the authors’ publication![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

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[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/05\/Screenshot-2025-05-08-at-11.54.54\u202fAM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] With the increase in high resolution imaging for histological analyses, Alec Soronow and colleagues from the Kim Neuroscience Lab at UC Santa Cruz have developed Bell […]<\/p>\n","protected":false},"author":3703,"featured_media":4339,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[167,170],"project_tag":[2372,2361,2320,763,762,805],"class_list":["post-4337","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-data-analysis-software","project_category-neural-signal-analysis","project_tag-analysis-pipeline","project_tag-atlas-registration","project_tag-histology","project_tag-mice","project_tag-mouse","project_tag-software"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4337","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/3703"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4337"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4337\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4339"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4337"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4337"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4337"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4331,"date":"2025-04-23T16:27:56","date_gmt":"2025-04-23T16:27:56","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4331"},"modified":"2025-04-23T16:27:57","modified_gmt":"2025-04-23T16:27:57","slug":"stposenet","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/stposenet\/","title":{"rendered":"STPoseNet"},"content":{"rendered":"

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Traditional methods for understanding animal behavior through videos required experimenters to rewatch videos and manually score timing and location of events. This approach is time consuming, and prone to inconsistencies between different scorers. Pose estimation methods have become widely used and can address the concerns of traditional methods by detecting underlying patterns in animal behavior. However, manual scoring can still be necessary at times, particularly in instances where video quality may be poor, such as in water maze experiments.<\/div>\n
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To address issues related to accuracy, processing speed, and annotation cost, Songyan Lv and colleagues collaborating from Guangxi University and Chongqing University have developed spatiotemporal PoseNet (STPoseNet). STPoseNet is a mouse pose estimation tool that is based on the YOLOv8 model, an established image recognition model that is capable of real-time accuracy, even in settings with complex backgrounds.\u00a0 STPoseNet has high accuracy thanks to its tracking-cropping module (TCM), which uses timing information for key point detection. It also has a Kalman filter-based module, which can predict key points in consecutive frames to account for any missing data during the experiment.<\/div>\n
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STPoseNet has high accuracy, fast processing, and minimal labeling (<100 images needed for a single experimental scenario). It has been validated for mouse pose estimation both in open field and water maze settings, making it suitable for a wide array of behavioral experiments.<\/div>\n
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This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications.\u00a0<\/i><\/span>RRID:SCR_026834<\/i><\/div>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the files!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/lvrgb777\/STPoseNet” link_option_url_new_window=”on”]<\/p>\n

All software files are available in a GitHub repository.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2589004224009945″ link_option_url_new_window=”on”]Find out more in the authors’ publication![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

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[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/04\/Screenshot-2025-04-23-at-12.02.39\u202fPM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] Traditional methods for understanding animal behavior through videos required experimenters to rewatch videos and manually score timing and location of events. This approach is time consuming, […]<\/p>\n","protected":false},"author":3703,"featured_media":4332,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[153,167,168,169,156],"project_tag":[2187,2410,763,762,2243,805,797,2406],"class_list":["post-4331","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-measurement","project_category-data-analysis-software","project_category-video-analysis-data-analysis","project_category-behavior-analysis","project_category-freely-moving","project_tag-behavior","project_tag-behavior-measurement","project_tag-mice","project_tag-mouse","project_tag-pose-estimation","project_tag-software","project_tag-video","project_tag-video-analysis"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4331","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/3703"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4331"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4331\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4332"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4331"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4331"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4331"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4321,"date":"2025-04-11T16:44:20","date_gmt":"2025-04-11T16:44:20","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4321"},"modified":"2025-06-26T17:43:28","modified_gmt":"2025-06-26T17:43:28","slug":"kinewheelarena-dlc","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/kinewheelarena-dlc\/","title":{"rendered":"KineWheelArena-DLC"},"content":{"rendered":"

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Bj\u00f6rn Albrecht and colleagues in the lab of York Winter from Humboldt Universit\u00e4t<\/a> have developed an innovative system that enhances the efficiency of markerless pose estimation. Their method integrates existing technologies like KineWheel and DeepLabCut, specifically addressing one of the most time-consuming steps: the manual labeling of training frames.\u00a0<\/span><\/p>\n

The system\u2019s design alternates between two types of illumination, standard white light and ultraviolet (UV) light, at a high frame rate. As mice move on a specialized transparent wheel, their paws (treated with safe fluorescent dye) briefly fluoresce under UV flashes. These illuminated frames reveal precise paw positions, which the system uses to label corresponding white-light frames through a Python script. Early testing of this toolkit add-on demonstrates that the high accuracy expected from markerless tracking is maintained, while drastically reducing manual labeling work.<\/span><\/p>\n

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications.\u00a0<\/span><\/i><\/span>RRID is currently pending, stay tuned!<\/i><\/p>\n

\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the code!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/WinterLab-Berlin\/KineWheelSystem” link_option_url_new_window=”on”]<\/p>\n

All design files are available in a GitHub repository.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.eneuro.org\/content\/11\/8\/ENEURO.0304-23.2024″ link_option_url_new_window=”on”]Find out more in the authors’ publication![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

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[\/et_pb_text][et_pb_divider color=”#ffffff” divider_position=”center” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_portfolio fullwidth=”off” posts_number=”4″ include_categories=”173″ show_categories=”off” zoom_icon_color=”rgba(0,0,0,0)” hover_overlay_color=”rgba(0,0,0,0)” _builder_version=”3.26.3″ title_level=”h6″ background_color=”#121212″ text_orientation=”left” locked=”off”][\/et_pb_portfolio][\/et_pb_column][et_pb_column type=”2_5″ _builder_version=”3.26.3″][et_pb_contact_form captcha=”off” email=”openbehavior@gmail.com” title=”Have questions? Send us an email!” success_message=”Thanks! We’ll try and get back to you soon!” _builder_version=”3.26.3″ title_level=”h3″ title_font=”|600|||||||” title_text_align=”center” title_font_size=”19px” captcha_text_color=”#ffffff” captcha_font_size=”46px” custom_button=”on” button_text_size=”13px” button_text_color=”#ffffff” button_bg_color=”#000000″ text_orientation=”left” custom_margin=”20px||10px||false|false” custom_padding=”5px|5px|5px|5px|false|false”][et_pb_contact_field field_id=”Name” field_title=”Name” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Email” field_title=”Email Address” field_type=”email” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Message” field_title=”Message” field_type=”text” fullwidth_field=”on” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][\/et_pb_contact_form][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/04\/Screen-Shot-2025-04-10-at-12.26.05-PM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] Bj\u00f6rn Albrecht and colleagues in the lab of York Winter from Humboldt Universit\u00e4t have developed an innovative system that enhances the efficiency of markerless pose estimation. […]<\/p>\n","protected":false},"author":4165,"featured_media":4322,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[171,153,167,168,169,155,174],"project_tag":[2418,807,2411,763,762,795],"class_list":["post-4321","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-apparatus","project_category-behavior-measurement","project_category-data-analysis-software","project_category-video-analysis-data-analysis","project_category-behavior-analysis","project_category-head-fixed","project_category-integrated-systems","project_tag-deeplabcut","project_tag-hardware","project_tag-head-fixed","project_tag-mice","project_tag-mouse","project_tag-python"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4321","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/4165"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4321"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4321\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4322"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4321"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4321"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4321"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4315,"date":"2025-03-27T18:36:14","date_gmt":"2025-03-27T18:36:14","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4315"},"modified":"2025-03-27T18:36:16","modified_gmt":"2025-03-27T18:36:16","slug":"myvivarium","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/myvivarium\/","title":{"rendered":"MyVivarium"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/03\/Screenshot-2025-03-26-at-2.40.25\u202fPM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

Researchers from the Sathyanesan Lab<\/span><\/a> at the University of Dayton have introduced MyVivarium, an open source tool for managing animal colonies. Through an online web application that is easily deployed to cloud, all lab members may track individual animals by mapping cages into the data base through QR codes on mobile devices. The application can also assist with lab management, including tracking tasks that are needed for cage maintenance and sending reminders for experiments. MyVivarium is easily implemented and provides a low-cost\u00a0 solution to less efficient means of tracking vivaria, such as using spreadsheets to manually track conditions. Additionally, the group developed IoT sensors which monitor environmental conditions of the vivarium including humidity, temperature, and illuminance.<\/p>\n

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This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications. MyVivarium: <\/i><\/span>RRID:SCR_026660; IoT sensors: RRID:SCR_026661<\/em><\/span><\/p>\n

\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_3,1_3,1_3″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”MyVivarium repository” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/myvivarium\/MyVivarium” link_option_url_new_window=”on”][\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”IoT Sensors repository” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/github.com\/myvivarium\/RPi-IoT” link_option_url_new_window=”on”][\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”3.26.3″][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2001037025000261″ link_option_url_new_window=”on”]Read more in the publication![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

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[\/et_pb_text][et_pb_divider color=”#ffffff” divider_position=”center” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_portfolio fullwidth=”off” posts_number=”4″ include_categories=”173″ show_categories=”off” zoom_icon_color=”rgba(0,0,0,0)” hover_overlay_color=”rgba(0,0,0,0)” _builder_version=”3.26.3″ title_level=”h6″ background_color=”#121212″ text_orientation=”left” locked=”off”][\/et_pb_portfolio][\/et_pb_column][et_pb_column type=”2_5″ _builder_version=”3.26.3″][et_pb_contact_form captcha=”off” email=”openbehavior@gmail.com” title=”Have questions? Send us an email!” success_message=”Thanks! We’ll try and get back to you soon!” _builder_version=”3.26.3″ title_level=”h3″ title_font=”|600|||||||” title_text_align=”center” title_font_size=”19px” captcha_text_color=”#ffffff” captcha_font_size=”46px” custom_button=”on” button_text_size=”13px” button_text_color=”#ffffff” button_bg_color=”#000000″ text_orientation=”left” custom_margin=”20px||10px||false|false” custom_padding=”5px|5px|5px|5px|false|false”][et_pb_contact_field field_id=”Name” field_title=”Name” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Email” field_title=”Email Address” field_type=”email” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Message” field_title=”Message” field_type=”text” fullwidth_field=”on” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][\/et_pb_contact_form][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/03\/Screenshot-2025-03-26-at-2.40.25\u202fPM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] Researchers from the Sathyanesan Lab at the University of Dayton have introduced MyVivarium, an open source tool for managing animal colonies. Through an online web application […]<\/p>\n","protected":false},"author":3703,"featured_media":4316,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[154,174],"project_tag":[790,2172,762,2179,760,761,2221,2242,2417],"class_list":["post-4315","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-homecage","project_category-integrated-systems","project_tag-automated","project_tag-home-cage","project_tag-mouse","project_tag-multiple-animals","project_tag-rat","project_tag-rodent","project_tag-single-animals","project_tag-tracking","project_tag-vivarium"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4315","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/3703"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4315"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4315\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4316"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4315"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4315"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4315"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4310,"date":"2025-03-13T16:13:48","date_gmt":"2025-03-13T16:13:48","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4310"},"modified":"2025-03-13T16:13:50","modified_gmt":"2025-03-13T16:13:50","slug":"aruco-markers","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/aruco-markers\/","title":{"rendered":"ArUco Markers"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/03\/Screenshot-2025-03-13-at-12.01.32\u202fPM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

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ArUco (“Augmented Reality University of Cordoba”) Markers were developed by Thomas Smith and Trevor Smith in a joint effort with collaborators from the University of Texas at Dallas, West Virginia University, and Case Western Reserve University. These markers provide an automated method for scoring animal behavior, specifically in a go\/no-go task. This reduces the dependence on video methods for behavioral scoring, which can be time consuming and prone to user bias.<\/p>\n

The ArUco marker can be mounted to an animal’s head, and fits onto an animals headcap while they are tethered. Then, the system monitors behavioral engagement using open-source software. 3D design files and necessary software has been made available, as well as code that can be used for data analysis. When validated against video data, ArUco markers were shown to have 98% accuracy when classifying behavioral engagement versus distraction. An additional benefit to this system is the ability to determine the optimal length of behavioral testing. Through classifying behavioral engagement, the group determined that animals become disengaged in a go\/no-go task around ~75 minutes.\u00a0 ArUco markers provide a simple and automated solution for behavioral scoring, with the added benefit of finding optimal testing durations.<\/p>\n<\/div>\n

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This research tool was created by your colleagues. Please acknowledge the Principal Investigator and cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications. RRID: SCR_<\/i><\/span>SCR_026572<\/i><\/p>\n<\/div>\n

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[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the code!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/tomcatsmith19\/ArucoDetection” link_option_url_new_window=”on”]<\/p>\n

Software and 3D design files available in a GitHub repository.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”3.26.3″][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.eneuro.org\/content\/11\/3\/ENEURO.0500-23.2024″ link_option_url_new_window=”on”]Find out more in the authors’ paper![\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

Check out projects similar to this!<\/p>\n

[\/et_pb_text][et_pb_divider color=”#ffffff” divider_position=”center” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_portfolio fullwidth=”off” posts_number=”4″ include_categories=”173″ show_categories=”off” zoom_icon_color=”rgba(0,0,0,0)” hover_overlay_color=”rgba(0,0,0,0)” _builder_version=”3.26.3″ title_level=”h6″ background_color=”#121212″ text_orientation=”left” locked=”off”][\/et_pb_portfolio][\/et_pb_column][et_pb_column type=”2_5″ _builder_version=”3.26.3″][et_pb_contact_form captcha=”off” email=”openbehavior@gmail.com” title=”Have questions? Send us an email!” success_message=”Thanks! We’ll try and get back to you soon!” _builder_version=”3.26.3″ title_level=”h3″ title_font=”|600|||||||” title_text_align=”center” title_font_size=”19px” captcha_text_color=”#ffffff” captcha_font_size=”46px” custom_button=”on” button_text_size=”13px” button_text_color=”#ffffff” button_bg_color=”#000000″ text_orientation=”left” custom_margin=”20px||10px||false|false” custom_padding=”5px|5px|5px|5px|false|false”][et_pb_contact_field field_id=”Name” field_title=”Name” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Email” field_title=”Email Address” field_type=”email” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Message” field_title=”Message” field_type=”text” fullwidth_field=”on” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][\/et_pb_contact_form][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/03\/Screenshot-2025-03-13-at-12.01.32\u202fPM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] ArUco (“Augmented Reality University of Cordoba”) Markers were developed by Thomas Smith and Trevor Smith in a joint effort with collaborators from the University of Texas […]<\/p>\n","protected":false},"author":3703,"featured_media":4311,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[153,167,168,169,156],"project_tag":[2334,790,2187,2409,2273,807,761,805,2242],"class_list":["post-4310","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-measurement","project_category-data-analysis-software","project_category-video-analysis-data-analysis","project_category-behavior-analysis","project_category-freely-moving","project_tag-3d-printing","project_tag-automated","project_tag-behavior","project_tag-freely-moving","project_tag-go-no-go","project_tag-hardware","project_tag-rodent","project_tag-software","project_tag-tracking"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4310","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/3703"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4310"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4310\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4311"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4310"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4310"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4310"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4305,"date":"2025-03-06T17:55:18","date_gmt":"2025-03-06T17:55:18","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4305"},"modified":"2025-06-26T17:44:09","modified_gmt":"2025-06-26T17:44:09","slug":"mesopy","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/mesopy\/","title":{"rendered":"Meso-Py"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/03\/Screen-Shot-2025-03-06-at-11.48.00-AM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

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Nicholas Michelson and colleagues, in the lab of Timothy Murphy at the University of British Columbia, developed Meso-Py. It is a Raspberry-Pi based platform for dual-brain calcium imaging in mice during head-fixed social interactions. Designed to explore the neural mechanisms of social behavior, Meso-Py enables simultaneous monitoring of neural activity in two mice, combining widefield mesoscopic imaging with customizable social stimuli. This system captures large-scale cortical dynamics with high temporal and spatial resolution, providing a powerful tool for studying brain-wide activity during naturalistic behaviors. Validation experiments demonstrated the platform\u2019s ability to reliably capture cortical activity patterns during social interactions, confirming its reliability for studying brain-wide dynamics. Hardware documentation, software, and protocols are provided, allowing researchers to replicate and customize the device easily.\u00a0<\/span><\/p>\n

This research tool was created by your colleagues. Please acknowledge the Principal Investigator, cite the article in which the tool was described, and include an RRID in the Materials and Methods of your future publications. RRID: SCR_026530<\/i><\/span><\/p>\n

\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”][et_pb_row column_structure=”1_3,1_3,1_3″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the code!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/ubcbraincircuits\/dual-mouse” link_option_url_new_window=”on”]<\/p>\n

Data Acquisition and Analysis code available in a GitHub repository.<\/p>\n

[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the design files!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2021\/05\/OSF.jpeg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/osf.io\/afuzn\/” link_option_url_new_window=”on”]All hardware documentation and assembly instructions available on OSF.[\/et_pb_blurb][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”3.26.3″][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.eneuro.org\/content\/10\/12\/ENEURO.0096-23.2023″ link_option_url_new_window=”on”]<\/p>\n

Find out more in the authors’ publication!<\/p>\n

[\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

Check out projects similar to this!<\/p>\n

[\/et_pb_text][et_pb_divider color=”#ffffff” divider_position=”center” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_portfolio fullwidth=”off” posts_number=”4″ include_categories=”173″ show_categories=”off” zoom_icon_color=”rgba(0,0,0,0)” hover_overlay_color=”rgba(0,0,0,0)” _builder_version=”3.26.3″ title_level=”h6″ background_color=”#121212″ text_orientation=”left” locked=”off”][\/et_pb_portfolio][\/et_pb_column][et_pb_column type=”2_5″ _builder_version=”3.26.3″][et_pb_contact_form captcha=”off” email=”openbehavior@gmail.com” title=”Have questions? Send us an email!” success_message=”Thanks! We’ll try and get back to you soon!” _builder_version=”3.26.3″ title_level=”h3″ title_font=”|600|||||||” title_text_align=”center” title_font_size=”19px” captcha_text_color=”#ffffff” captcha_font_size=”46px” custom_button=”on” button_text_size=”13px” button_text_color=”#ffffff” button_bg_color=”#000000″ text_orientation=”left” custom_margin=”20px||10px||false|false” custom_padding=”5px|5px|5px|5px|false|false”][et_pb_contact_field field_id=”Name” field_title=”Name” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Email” field_title=”Email Address” field_type=”email” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][et_pb_contact_field field_id=”Message” field_title=”Message” field_type=”text” fullwidth_field=”on” _builder_version=”3.16″ border_radii=”on||||” button_text_size__hover_enabled=”off” button_one_text_size__hover_enabled=”off” button_two_text_size__hover_enabled=”off” button_text_color__hover_enabled=”off” button_one_text_color__hover_enabled=”off” button_two_text_color__hover_enabled=”off” button_border_width__hover_enabled=”off” button_one_border_width__hover_enabled=”off” button_two_border_width__hover_enabled=”off” button_border_color__hover_enabled=”off” button_one_border_color__hover_enabled=”off” button_two_border_color__hover_enabled=”off” button_border_radius__hover_enabled=”off” button_one_border_radius__hover_enabled=”off” button_two_border_radius__hover_enabled=”off” button_letter_spacing__hover_enabled=”off” button_one_letter_spacing__hover_enabled=”off” button_two_letter_spacing__hover_enabled=”off” button_bg_color__hover_enabled=”off” button_one_bg_color__hover_enabled=”off” button_two_bg_color__hover_enabled=”off”][\/et_pb_contact_field][\/et_pb_contact_form][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/03\/Screen-Shot-2025-03-06-at-11.48.00-AM.png” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] Nicholas Michelson and colleagues, in the lab of Timothy Murphy at the University of British Columbia, developed Meso-Py. It is a Raspberry-Pi based platform for dual-brain […]<\/p>\n","protected":false},"author":4165,"featured_media":4299,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[171,173,172,155,174],"project_tag":[2334,807,763,762,2171],"class_list":["post-4305","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-apparatus","project_category-behavior-rigs","project_category-behavioral-tasks","project_category-head-fixed","project_category-integrated-systems","project_tag-3d-printing","project_tag-hardware","project_tag-mice","project_tag-mouse","project_tag-raspberry-pi"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4305","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/4165"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4305"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4305\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4299"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4305"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4305"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4305"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}},{"id":4295,"date":"2025-02-28T20:12:43","date_gmt":"2025-02-28T20:12:43","guid":{"rendered":"https:\/\/edspace.american.edu\/openbehavior\/?post_type=project&p=4295"},"modified":"2025-03-06T17:53:34","modified_gmt":"2025-03-06T17:53:34","slug":"flexrig","status":"publish","type":"project","link":"https:\/\/edspace.american.edu\/openbehavior\/project\/flexrig\/","title":{"rendered":"FlexRig"},"content":{"rendered":"

[et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/02\/F2.large_.jpg” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”]<\/p>\n

\n

FlexRig<\/strong> is an open-source platform for running experiments to test decision making and cognitive flexibility in mice. It was developed by Dr Tim Spellman<\/a> and his lab at the UConn School of Medicine. The platform allows for using olfactory, somatosensory, and\/or auditory cues and directional licking responses as a behavior readout.<\/p>\n

The platform offers a stand-alone testing setup, and could be scaled or modified for other uses thanks to the full sharing of the design files and programs needed to build and use the platform. Hardware modules include the following six components:<\/p>\n

    \n
  1. A base for head-restraint<\/li>\n
  2. A module for delivering liquid rewards<\/li>\n
  3. A module for translating left\/right licks into behavioral readouts<\/li>\n
  4. A module for delivering of up to four odorants in a given experimental design<\/li>\n
  5. A module for delivering auditory (\u223c5\u201320\u2005KHz stimuli) and\/or whisker somatosensory (20\u2013300\u2005Hz stimuli) cues<\/li>\n
  6. A command stage for interfacing the hardware components with an Arduino control board<\/li>\n<\/ol>\n

    A set of Arduino programs is included for the control of all hardware modules and for programming behavioral experiments. This includes software for controlling optogenetics equipment and interfacing with electrical and\/or optical recording systems.<\/p>\n

    Build instructions are given in the published manuscript on the eNeuro<\/a> website. Required files are included with the manuscript as Extended Data and also in a GitHub<\/a> repository.<\/p>\n

    This is an outstanding example of sharing setups and protocols for neuroscience research. Such sharing provides rapid access to cutting edge tools used in ongoing research and enhances research rigor and reproducibility. We are not aware of any integrated system such as FlexRig from any commercial vendors, and the required hardware is readily available from makerspace vendors such as Arduino and other resources listed on our Resources<\/a> page. This makes FlexRig a low-cost and fully capable system, and it might be useful for your research!<\/p>\n

    The paper at eNeuro<\/a> was highly lauded by the reviewers and handling editor. This lead the Society for Neuroscience to select the paper for an upcoming webinar on FlexRig and open-source tools in general. The webinar will be on March 25 from 11:45 am \u2013 1 pm ET. Here is the registration page for this webinar: https:\/\/neuronline.sfn.org\/scientific-research\/an-open-source-3d-printable-platform<\/a>. If you are not a member of SfN, please contact the OpenBehavior project at openbehavior@gmail.com<\/a> for a code to attend the webinar.<\/p>\n

    This research tool was created by your colleagues. Please acknowledge the Principal Investigator and cite the article in which the tool was described.<\/i><\/p>\n<\/div>\n

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    \n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n<\/div>\n

    [\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n

    [et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ min_height=”820.9px” custom_margin=”-232px||-268px|||” custom_padding=”0px|||||”]<\/p>\n

    [et_pb_row column_structure=”1_2,1_2″ custom_padding=”5px|5px|5px|5px|false|false” _builder_version=”3.26.3″ min_height=”251.5px” locked=”off”]<\/p>\n

    [et_pb_column type=”1_2″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_blurb title=”Access the code!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2020\/01\/github-logo.jpg” image_max_width=”80%” _builder_version=”3.26.3″ custom_padding=”5px|5px|5px|5px|false|false” link_option_url=”https:\/\/github.com\/spellmanlab\/FlexRig” link_option_url_new_window=”on”]<\/p>\n

    Software available in a GitHub repository.<\/p>\n

    [\/et_pb_blurb][\/et_pb_column]<\/p>\n

    [et_pb_column type=”1_2″ _builder_version=”3.26.3″][et_pb_blurb title=”Read more about it!” url_new_window=”on” image=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/1502\/2020\/01\/business-4561935_1280.jpg” image_max_width=”73%” _builder_version=”3.26.3″ background_color=”rgba(0,0,0,0)” link_option_url=”https:\/\/www.eneuro.org\/content\/12\/1\/ENEURO.0364-24.2024″ link_option_url_new_window=”on”]<\/p>\n

    Find out more in the authors’ paper!<\/p>\n

    [\/et_pb_blurb][\/et_pb_column][\/et_pb_row][\/et_pb_section]<\/p>\n

    [et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″][et_pb_row column_structure=”3_5,2_5″ _builder_version=”3.26.3″][et_pb_column type=”3_5″ _builder_version=”3.26.3″][et_pb_text _builder_version=”3.26.3″ text_font=”|600|||||||” text_font_size=”24px”]<\/p>\n

    Check out projects similar to this!<\/p>\n

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    [et_pb_section fb_built=”1″ _builder_version=”3.26.3″ background_color=”#121212″ custom_padding=”0″ background_last_edited=”off|desktop” background__hover_enabled=”off”][et_pb_row custom_padding=”4em|||||” custom_margin=”auto|auto” _builder_version=”3.26.3″ width=”86.3%”][et_pb_column type=”4_4″ _builder_version=”3.26.3″][et_pb_post_title author=”off” comments=”off” featured_image=”off” _builder_version=”3.26.3″ title_text_align=”center” meta_text_align=”center”][\/et_pb_post_title][et_pb_divider color=”#ffffff” _builder_version=”3.26.3″][\/et_pb_divider][et_pb_image src=”http:\/\/edspace.american.edu\/openbehavior\/wp-content\/uploads\/sites\/2431\/2025\/02\/F2.large_.jpg” _builder_version=”3.26.3″ max_width=”40%” module_alignment=”center”][\/et_pb_image][et_pb_text _builder_version=”3.26.3″ min_height=”402px” custom_padding=”2em|0|0|0″ link_option_url_new_window=”on”] FlexRig is an open-source platform for running experiments to test decision making and cognitive flexibility in mice. It was developed by Dr Tim Spellman and his […]<\/p>\n","protected":false},"author":2065,"featured_media":4304,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","jetpack_post_was_ever_published":true,"footnotes":""},"project_category":[171,153,148,173,172,150,155,174,152,175,176],"project_tag":[2334,790,2187,2212,2409,807,2268,761],"class_list":["post-4295","project","type-project","status-publish","has-post-thumbnail","hentry","project_category-behavior-apparatus","project_category-behavior-measurement","project_category-neural-recording","project_category-behavior-rigs","project_category-behavioral-tasks","project_category-electrical-recording","project_category-head-fixed","project_category-integrated-systems","project_category-optical-imaging","project_category-reward-delivery","project_category-stimuli","project_tag-3d-printing","project_tag-automated","project_tag-behavior","project_tag-elevated-plus-maze","project_tag-freely-moving","project_tag-hardware","project_tag-maze","project_tag-rodent"],"jetpack_sharing_enabled":true,"_links":{"self":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4295","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project"}],"about":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/types\/project"}],"author":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/users\/2065"}],"replies":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/comments?post=4295"}],"version-history":[{"count":0,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project\/4295\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media\/4304"}],"wp:attachment":[{"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/media?parent=4295"}],"wp:term":[{"taxonomy":"project_category","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_category?post=4295"},{"taxonomy":"project_tag","embeddable":true,"href":"https:\/\/edspace.american.edu\/openbehavior\/wp-json\/wp\/v2\/project_tag?post=4295"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}]