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http://cellprofiler.org

Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.

Proper citation: CellProfiler Image Analysis Software (RRID:SCR_007358) Copy   

•   Source: SciCrunch Registry

http://www.gepas.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. An integrated packages of tools for microarray data analysis. GEPAS provides a web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-color microarray experiments and other preprocessing options), to the final step of the functional profiling of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), which include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management.

Proper citation: Gene Expression Profile Analysis Suite (RRID:SCR_008341) Copy   

•   Source: SciCrunch Registry

https://compumedicsneuroscan.com/products/by-name/curry/

Processing software for multimodal neuroimaging centered on combining functional data such as EEG and MEG with imaging data from MRI and CT to optimize source reconstruction. They are now combining Curry's strength with the acquisition and signal processing features of the SCAN software for a comprehensive EEG acquisition, data analysis, source localization and source imaging package.

Proper citation: CURRY (RRID:SCR_009546) Copy   

•   Source: SciCrunch Registry

http://marsbar.sourceforge.net/

A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery.

Proper citation: MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) Copy   

•   Source: SciCrunch Registry

http://mrtools.mgh.harvard.edu/index.php/TBR

A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.

Proper citation: Template Based Rotation (RRID:SCR_012157) Copy   

•   Source: SciCrunch Registry

http://openbabel.org/wiki/Main_Page

Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats.

Proper citation: Open Babel (RRID:SCR_014920) Copy   

•   Source: SciCrunch Registry

http://www.ccb.jhu.edu/

Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis.

Proper citation: Center for Computational Biology at JHU (RRID:SCR_016680) Copy   

•   Source: SciCrunch Registry

http://www.reproducibleimaging.org

Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible.

Proper citation: ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) Copy   

•   Source: SciCrunch Registry

http://oufti.org/

Software designed for analysis of microscopy data. It performs sub-pixel precision detection, quantification of cells and fluorescence signals, as well as other image analysis functions.

Proper citation: Oufti (RRID:SCR_016244) Copy   

•   Source: SciCrunch Registry

https://github.com/YuanXue1993/SegAN

Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps.

Proper citation: SegAN (RRID:SCR_016215) Copy   

•   Source: SciCrunch Registry

https://cryosparc.com/

Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery.

Proper citation: cryoSPARC (RRID:SCR_016501) Copy   

•   Source: SciCrunch Registry

https://wholetale.org/

Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility.

Proper citation: Whole Tale (RRID:SCR_017537) Copy   

•   Source: SciCrunch Registry

https://www.keyence.co.jp/products/microscope/fluorescence-microscope/bz-x700/models/bz-h3a/

Software tool as analysis application BZ-H3A by Keyence, Osaka, Japan for fluorescence microscope BZ-X series.

Proper citation: BZ-H3A analyzer software (RRID:SCR_017375) Copy   

•   Source: SciCrunch Registry

https://github.com/fritzsedlazeck/Sniffles

Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates.

Proper citation: Sniffles (RRID:SCR_017619) Copy   

•   Source: SciCrunch Registry

https://www.silkscientific.com/gel-analysis.htm

Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC.

Proper citation: UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/stereo-investigator-whole-slide-edition

Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses.

Proper citation: Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) Copy   

•   Source: SciCrunch Registry

https://www.essenbioscience.com/en/products/software/incucyte-chemotaxis-software/

IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate.

Proper citation: IncuCyte® Chemotaxis Software (RRID:SCR_017316) Copy   

•   Source: SciCrunch Registry

http://www.imgt.org/StatClonotype/

Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences.

Proper citation: IMGT/StatClonotype (RRID:SCR_018963) Copy   

•   Source: SciCrunch Registry

https://github.com/auranic/ClinTrajan

Software Python package for analysis of trajectories in clinical datasets.

Proper citation: ClinTrajAn (RRID:SCR_019018) Copy   

•   Source: SciCrunch Registry

https://github.com/MRCIEU/TwoSampleMR

Software R package for performing Mendelian randomization using genome wide association study summary data.

Proper citation: TwoSampleMR (RRID:SCR_019010) Copy   

•   Source: SciCrunch Registry