Open-Source Tools for Data Analysis

Feb 13, 2025 | Community Call to Action, In the Community, Open Source Resource, Uncategorized

Open-Source Tools for Data Analysis

This year, we’re focusing on the impact of open-source tools on research productivity, which seems especially relevant given current funding challenges for science. Our findings aim to demonstrate how collaborative, open efforts are increasing research capacity and efficiency within neuroscience. Low-cost solutions are crucial in this era of increasing financial austerity for biomedical research.

Over the past four years, we published 322 posts on 266 open-source research tools and 56 posts on other resources, including training workshops and our video and 3D printing repositories. To categorize these tools, we created a database with six categories:

  • Behavior Apparatus: Tools and devices used to build or supplement behavioral rigs. While some projects are fully developed rigs, their open-source nature allows for flexible adaptation and integration into existing systems.
  • Behavior Measurement: Devices and programs designed to quantify aspects of behavior, providing a quantifiable readout.
  • Data Analysis: Software packages for analyzing behavioral data, video recordings, neural activity, and histological images.
  • Neural Modulation: Primarily hardware for modulating neural activity using drugs, light, or electrical stimulation.
  • Neural Recording: Tools, including electrodes and associated hardware and software, for collecting and analyzing neural data.
  • Video Recording & Analysis: Options for video-based behavior tracking (real-time and pre-recorded) across various species, along with specialized video recording hardware.

Our database reveals that the majority of the 266 projects focus on data analysis, closely followed by tools for quantitative behavior measurement (Figure 1A). Website traffic from Summer 2021 to Summer 2024 confirms this trend, with these two categories receiving the most page hits (Figure 1B).

Figure 1

This initial report highlights the Data Analysis category, which comprises two equally popular tool types among our audience. The first type focuses on video recording analysis (Figure 2). The top five projects in this subcategory are well-established within the research community: Simba, Eztrack, Deeplabcut, Sleap, and Boris.

Figure 2
  • Simba: A set of programs designed for analyzing pose estimation data, enabling the study of social interactions in rodents without manual scoring. Its modular design facilitates adaptation to diverse research questions, providing an accessible entry point for non-programmers working with video pose methods and machine learning for behavior classification.
  • Eztrack: A “blob tracker” that efficiently tracks moving objects (e.g., rodents) against a contrasting background. Simple to set up and use, it has been successfully implemented in behavioral neuroscience teaching labs, including at our host university, by TAs and students with limited programming experience.
  • Deeplabcut and Sleap: Programs used for pose estimation, which can automatically identify and track the body parts of animals in video recordings. These programs are gateways to more advanced methods for video analysis.
  • Boris: A standalone program offering a user-defined coding environment for computer-based review of recorded videos or live observations. Developed for behavioral biology, Boris is also valuable in neuroscience, particularly for scoring specific behaviors, such as home cage activity.

The second type of data analysis software includes standalone programs and code incorporated into some hardware platforms (Figure 3), showcasing the diverse research areas benefiting from open-source tools. The top five projects in this category include three packages for brain histology data analysis (Fastmap, Brainways, and Wholebrain), previously featured in our 2024 end-of-the-year review of open-source tools. These tools address critical needs often unmet by commercial vendors, generating significant interest within the research community.

Figure 3

Other popular platforms in this category include:

  • Bpod: An early Open Behavior (OB) project from 2017, developed by Josh Sanders and Sanworks. Bpod is a measurement and control system for behavioral research, continuously evolving and currently available in release 2+ at https://sanworks.io, alongside other open-source tools.
  • SipperViz: A Python-based GUI for visualizing data from Sippers, a 3D-printed, open-source device for measuring liquid ingestion in rodents. Developed by Tom Earnest from the Creed and Kravitz Labs at Washington University, SipperViz quantifies the frequency and duration of ingestion bouts.

Project Links

Video Software:

Other Software: