Behavioral Analysis Toolkit

• SLEAP

  • https://sleap.ai/

  • My go-to GPU-based tracking software. I much prefer this interface over DLC due to it's human in the loop training features, fast training times with loss-plateu cut-offs,  and easy to use skeleton  drawing features. Love this software!

  • Click here for my protocol [in active development]

• SIMBA

  • From Simon Nilsson and Sam Golden's Lab at UW, this software is another go-to for me for analyzing SLEAP and DLC output data files for movement dynamics, time spent in ROIs, and supervised and unsupervised behavioral classifiers. 

  • https://goldenneurolab.com/simba

  • Click here for my protocol [in active development]

• Deep Audio Segmenter (DAS)

  • A truly remarkable piece of software for segmenting out mouse ultrasonic vocalizations (or really, any "sound") from audio data. Deep neural network based approach, with a lightweight and fairly easy to learn GUI. Python based, and so open-source. Replaced DeepSqueak for my analysis. 

  • https://janclemenslab.org/das/index.html

  • Click here for my protocol [in active development]

• DeepLabCut (DLC)

  • Not my go-to, but still a solid piece of software that is used broadly by the neuroscience and behavior community. It changed the game when it came out!

  • https://github.com/DeepLabCut/DeepLabCut

• DeepSqueak

  • My previous go-to for USV detection analysis in mice. Feature rich, but purely MATLAB-based. 

  • https://github.com/DrCoffey/DeepSqueak

• ToxTrac

  • A stand-alone CPU-based multi-animal tracking software with a relatively simple GUI and ROI analysis capability. Best for videos of a single animal with a simple background or of low numbers of animals with no occlusions. Great for simple behavior tracking projects for undergrads who want to track short videos on their laptops (also pretty good in a classroom setting). 

  • https://sourceforge.net/projects/toxtrac/

• TrackR

  • An R-based 'classical' tracking program using OpenCV. Great for simple projects and for those new to programming/software generally.

  • https://github.com/swarm-lab/trackR

Neuroscience Toolkit

• https://brainmuseum.org/

  • Comparative brain anatomy across a variety of taxa with downloadable images, stains, slices, etc. 

• http://labs.gaidi.ca/mouse-brain-atlas/

  • Big shout out to Dr. Matt Gaidica for putting this out in the world. I use it all the time to check my stereotaxic surgery targeting. 

• https://ebrains.eu/services/atlases/

  • EU based brain atlases and other services. Nice 3D models here and GUI, especially if you check out via the siibra-explorer. 

• http://atlas.brain-map.org/

  • Allen Institute Brain Atlas, 3D and coronal slices available. 

• https://observatory.brain-map.org/visualcoding/

  • Allen Institute Brain Observatory data

• http://braininfo.rprc.washington.edu/Default.aspx

  • Nice site for quickly referencing unfamiliar brain regions. A bit outdated, but still useful! Links to the Allen toolkits for data. In some ways the GUI is more intuitive than the Allen interface!

• https://cic.ini.usc.edu/

  • Mouse Connectome Project from Larry Swanson's group at USC (and others). 

• https://sites.google.com/view/the-neurome-project/home

  • The Neurome Project from Larry Swanson

• https://mouselight.janelia.org/

  • From the folks at Janelia, you can use this to see the morphology of entire neurons across a 3D model of the brain. 

• https://neuprint.janelia.org/

  • From Janelia, drosophila connectomics explorer. Can also look at electron microscopy data. 

  • What can we learn about the Deep homology between vertebrates and invertebrates. 

  • Define cell types by connectivity, and neurotransmiters and other features. All trained via machine vision. Born from major research collaboration with google (and others)

• https://biccn.org/

  • NIH Brain Initiative Cell Census Network imaging and genomic data sets. 

• https://alphafold.ebi.ac.uk/

  • From the folks at DeepMind, great tool for checking the structure of proteins of interest.