Tools

Software, hardware designs, scripts, and other resources developed in the CPL.  As a rule, all packages are freely distributable; see individual listings below for license details. We build many of our own software tools for simulation and analysis — sometimes from scratch, but also by integrating and adapting tools and approaches designed by others and released under open source licenses.  We also build some of our own electronics hardware for customized behavioral testing.  Software tools, designs, and scripts with versions available for distribution can be examined by following the links in the Tools menu above.  Source code for published software and neural models is available from Github or ModelDB.

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  • Annolid is an annotation and instance segmentation-based multiple animal tracking and behavior analysis package. Annolid treats keypoints-based pose estimation as a special case of instance segmentation. Instance mask area and perimeter can be tracked, as well as keypoints. Read more here

  • Ceed is a Python based application to help run in-vitro experiments that optically stimulates brain slices and records their activity. Read more here

  • Filers2 is a tool that can play and record video from webcams and other media sources.

    It supports playing typical USB-WebCams and webstreams. It can also play from cameras such the Flir or Thor scientific cameras. Read more here

  • Glitter2 is an application for coding and analysing behavioral data from videos.

    It supports coding events with event channels, spatial tracking with position channels, and static zones with zone channels. Read more here

  • PyMoa is a framework for describing and running experiments using local or remote devices.

    It is composed of stages that determine the flow of an experiment, devices that interface with arbitrary hardware or software devices, loggers that automatically log all stage or device state changes, and executors that can run arbitrary devices on different threads, process, or even remote servers such as on a Raspberry-pi with minimal code changes. Read more here

  • Sapicore is a spiking neural network (SNN) simulator, built with PyTorch and designed for neuroscience-inspired models with realistic architectures and dynamics. Read more here

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