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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
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
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
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
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
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
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
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
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
https://github.com/caanlab/shiTools
Software tools for MRI and behavioral data analysis and visualization in MATLAB. SPM12/SPM25 is required for some of the functions.
Proper citation: shiTools (RRID:SCR_028886) Copy
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