The OpenBehavior Project primarily focuses on tools for behavioral testing and data analysis. However, our database also features a growing number of valuable open-source tools for imaging, including microscopy, calcium imaging, optical sensors, and integrated platforms for combining behavioral testing with imaging methods. This week’s post summarizes some of the top projects using these open-source technologies.
The word cloud above represents the top thirty tools in the “Imaging” category from our database, based on website traffic. Note that three highly impactful tools—Fastmap, Brainways, and Wholebrain—were featured in previous review posts and are not included in this word cloud.
The next top ten projects with the most page hits are:
- EZcalcium
- An automated MATLAB toolbox designed for the analysis of calcium imaging data.
- We posted about it in July 2021 (here).
- UCLA Miniscope
- An open-source and very widely used miniature fluorescence microscope, complete with integrated software and data interfacing.
- We posted about it in October 2016 (here).
- Mesoscale Imaging
- A homecage platform enabling automated task training combined with mesoscale brain imaging for mice.
- We posted about it in February 2021 (here).
- brainrender
- A Python package specifically for visualizing and interacting with datasets registered to brain atlases.
- We posted about it in September 2021 (here).
- ABA
- A FIJI-based tool for immunohistochemical analysis that allows for adjusting experimental images to published rat brain atlases.
- We posted about it in December 2021 (here).
- PyPhotometry
- An open-source and widely used system for fiber photometry. It includes a full graphical interface and a custom-made hardware interface.
- We posted about it in November 2022 (here).
- pMAT
- pMAT, or Photometry Modular Analysis Tool, is a MATLAB toolbox with a graphical interface for the analysis of fiber photometry data.
- We posted about it in July 2022 (here).
- pyOS-5
- An integrated hardware and Python-based software platform for operant testing, especially using 5-choice designs. It was optimized for use with tethered animals.
- We posted about it in December 2021 (here).
- NINscope
- A compact miniscope that integrates an inertial measurement sensor and an LED driver for optogenetic stimulation.
- We posted about it in September 2020 (here).
- M3 Platform
- A platform for simultaneous neuronal imaging and behavioral monitoring, based on hardware and software from Touchscreen Cognition and integrated with the UCLA Miniscope.
- We posted about it in March 2023 (here).