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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/cosanlab/facesync
Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.
Proper citation: FaceSync (RRID:SCR_021396) Copy
https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst
Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.
Proper citation: D-Track (RRID:SCR_021394) Copy
Open source software tool as file archiver with high compression ratio.
Proper citation: 7-Zip (RRID:SCR_021270) Copy
https://github.com/DeepLabCut/DeepLabCut
Open source software package for markerless pose estimation. 2D keypoint detection in animals.
Proper citation: DeepLabCut (RRID:SCR_021391) Copy
https://github.com/ModelOriented/randomForestExplainer
Software R package to help explain which variables are most important in random forests. Various variable importance measures are calculated and visualized in different settings in order to get idea on how their importance changes classification or regression model accuracy.
Proper citation: randomForestExplainer (RRID:SCR_021823) Copy
https://bioconductor.org/packages/karyoploteR/
Software R package used to karyoplots. Bioconductor package to plot customizable genomes displaying arbitrary data.
Proper citation: karyoploteR (RRID:SCR_021824) Copy
https://github.com/NollmannLab/qudi-HiM
Software package for control of optical microscope setups with different hardware components optimized to perform multiplexed imaging experiments. Modular laboratory experiment management suite.
Proper citation: qudi-HiM (RRID:SCR_022114) Copy
https://github.com/sqjin/CellChat
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
Proper citation: CellChat (RRID:SCR_021946) Copy
https://github.com/sdorkenw/MeshParty
Software package for working with neuronal meshes, skeletons, and annotations from electron microscopy data. Used to work with meshes, designed around use cases for analyzing neuronal morphology.
Proper citation: MeshParty (RRID:SCR_021873) Copy
https://github.com/leylabmpi/endoR/
Software R package to interpret fitted tree ensemble model.Used to extract and visualize how predictive variables contribute to tree ensemble model accuracy.
Proper citation: endoR (RRID:SCR_021916) Copy
https://github.com/wehr-lab/autopilot
Software tool as open source Python framework for behavioral neuroscience that distributes experiments over networked swarms of Raspberry Pis. Toolkit of flexible modules to design experiments without rigid programming and API limitations.
Proper citation: AutoPilot (RRID:SCR_021518) Copy
https://github.com/hietakangas-laboratory/LAM
Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.
Proper citation: Linear Analysis of Midgut (RRID:SCR_021255) Copy
https://iopscience.iop.org/article/10.1088/0957-0233/20/10/104035
Software package for advanced time domain analysis of magnetic resonance spectroscopy (MRS) and spectroscopic imaging (MRSI) data.
Proper citation: jMRUI (RRID:SCR_021893) Copy
https://github.com/oushujun/EDTA
Software package to filter out false discoveries in raw TE candidates and generate high quality non redundant TE library for whole genome TE annotations.Produces filtered non redundant TE library for annotation of structurally intact and fragmented elements.
Proper citation: EDTA (RRID:SCR_022063) Copy
https://github.com/jgraving/DeepPoseKit
Software toolkit with high level API for 2D pose estimation of user defined keypoints using deep learning.Written in Python and built using Tensorflow and Keras.Method for pose estimation developed by behavioral scientists at the Max Planck Institute of Animal Behavior.
Proper citation: DeepPoseKit (RRID:SCR_021405) Copy
https://neurokit2.readthedocs.io/en/latest/
Software Python package for neurophysiological signal processing. Used to analyze physiological data.
Proper citation: Neurokit2 (RRID:SCR_021889) Copy
https://github.com/DrCoffey/DeepSqueak
Software MATLAB package for high throughput ultrasonic vocalizations detection, classification, and analysis.
Proper citation: DeepSqueak (RRID:SCR_021524) Copy
https://knowledge.brain-map.org/celltypes
Software application to examine multimodal data from thousands of cells across 3 mammalian species.
Proper citation: Cell Type Knowledge Explorer (RRID:SCR_022793) Copy
https://github.com/Vaa3D/vaa3d_tools/tree/master/hackathon/mBrainAligner
Software package provides cross modality image registration pipeline to support whole brain mapping projects. Contains three modules: (1) image preprocessing and global registration, (2) Coherent Landmark Mapping (CLM) based automatic registration, and (3) optional semi-automatic refinement.
Proper citation: mBrainAligner (RRID:SCR_022791) Copy
https://www.millisecond.com/download/
Software tool for designing and administering psychological tests and experiments on computers.
Proper citation: Inquisit LAB (RRID:SCR_022151) Copy
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