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https://github.com/spm

Software package for analysis of brain imaging data sequences. Sequences can be a series of images from different cohorts, or time-series from same subject. Current release is designed for analysis of fMRI, PET, SPECT, EEG and MEG.

Proper citation: SPM (RRID:SCR_007037) Copy   

•   Source: SciCrunch Registry

https://github.com/NOCIONS/letswave6/wiki/Download-and-setup

Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.

Proper citation: Letswave (RRID:SCR_016414) Copy   

•   Source: SciCrunch Registry

https://www.mathworks.com/products/computer-vision.html

Software tool to provide algorithms, functions, and apps for designing and testing computer vision, 3D vision, and video processing systems for MATLAB. You can perform object detection and tracking, as well as feature detection, extraction, and matching. For 3D vision, toolbox supports single, stereo, and fisheye camera calibration; stereo vision; 3D reconstruction; and lidar and 3D point cloud processing. Computer vision apps automate ground truth labeling and camera calibration workflows.

Proper citation: Computer Vision System Toolbox (RRID:SCR_017581) Copy   

•   Source: SciCrunch Registry

https://github.com/zburkett/VoICE

Software that groups vocal elements of birdsong by creating a high dimensionality dataset through scoring spectral similarity between vocalizations.

Proper citation: Vocal Inventory Clustering Engine (VoICE) (RRID:SCR_016004) Copy   

•   Source: SciCrunch Registry

http://mtshasta.phys.washington.edu/website/SuperSegger.php

Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells.

Proper citation: SuperSegger (RRID:SCR_018532) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/PAM-PIE/PAM

Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities.

Proper citation: PAM (RRID:SCR_020966) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/p/iris-scanning/calliope

Software package for image processing for MATLAB. Used for processing of calcium imaging data.

Proper citation: Calliope calcium imaging processing package (RRID:SCR_021213) Copy   

•   Source: SciCrunch Registry

https://github.com/bahanonu/ciatah

Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.

Proper citation: calciumImagingAnalysis (RRID:SCR_021153) Copy   

•   Source: SciCrunch Registry

https://www.mayo.edu/research/labs/tissue-repair-mechanobiology/software

Software tool to calculate 2D tractions exerted by adherent cell on its substrate. Used in field of mechanobiology to study contractile responses of variety of cell types.

Proper citation: TractionsForAll (RRID:SCR_021819) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/efficient_pt

A Matlab implementation for efficient permutation testing by using matrix completion.

Proper citation: Efficient Permutation Testing (RRID:SCR_014104) Copy   

•   Source: SciCrunch Registry

https://github.com/colinvaz/nmf-toolbox

Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.

Proper citation: NMF Toolbox (RRID:SCR_017069) Copy   

•   Source: SciCrunch Registry

https://github.com/zhengkaiyu/FIMAS

Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files.

Proper citation: Fluorescent Imaging Analysis Software FIMAS (RRID:SCR_018311) Copy   

•   Source: SciCrunch Registry

https://github.com/nebneuron/neural-ideal

Software package for extracting neural activity codes.

Proper citation: Neural Ideal (RRID:SCR_017448) Copy   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry

https://github.com/KatrinSkerl/EvaluateMuscleTissueWithElastography/tree/main

Software tool that enables the automatic evaluation of muscle tissue on elastography imaging using MATLAB.

Proper citation: EvaluateMuscleTissueWithElastography (RRID:SCR_026737) Copy   

•   Source: SciCrunch Registry

https://github.com/GuyButcher/alpha-helix-coordinate-frame-simulation

Source code for alpha-helix simulation framework written in Matlab. Specifically tested on Talin-1 Rod Domain.

Proper citation: alpha helix coordinate frame simulation (RRID:SCR_019320) Copy   

•   Source: SciCrunch Registry

https://github.com/protofilamentdude/Protofilament-Bending-Models

Code is written to be run with Matlab version r2020b or higher. Model accepts wave assay pulse amplitude data, and simultaneously solves and fits protofilament deflection models to deduce fundamental biophysical properties of microtubule protofilaments.

Proper citation: Protofilament Bending Models (RRID:SCR_023062) Copy   

•   Source: SciCrunch Registry

https://github.com/keepersecond/Soma-Segmentation

Source code for a soma segmentation method suitable for datasets with touching soma distributions. The method contains three main parts: soma detection based on DT and local maximum searching and refining; an improved Rayburst sampling algorithm for isolated and touching soma surface detection; and ellipsoid fitting to generate the segmentation results.

Proper citation: Soma-Segmentation (RRID:SCR_015649) Copy   

•   Source: SciCrunch Registry

https://git.io/vAeKZ

It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.

Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy   

•   Source: SciCrunch Registry

https://github.com/missy139/PreSurgMapp

A MATLAB toolbox for processing the functional areas of the brain using multi-modal fMRI data for pre-surgical mapping. It is composed of three types of individual-level ICA analyses for user use. Traditional ICA (task) can be used for task fMRI. Either Traditional ICA (rest) or ICA with DICI (rest) can be used for rs-fMRI. Traditional ICA (rest) is designed for users who already have a hypothesis of the pattern of the target component and want to have manually set components by themselves. ICA with DICI (rest) is completely automatic, given that the user provides a template (provided). The software utilizes an automatic component identification method that is based on the discriminatory-index. All the components from multiple ICA runs with multiple component settings are ranked and compiled.

Proper citation: PreSurgMapp (RRID:SCR_014427) Copy   

•   Source: SciCrunch Registry