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https://emcore.ucsf.edu/cryoem-software

Software tool for anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Used to describe the sample motion as a local deformation that varies smoothly throughout the exposure. A program running on Linux.

Proper citation: MotionCor2 (RRID:SCR_016499) Copy   

•   Source: SciCrunch Registry

https://github.com/mizutanilab/MCTrace

Software tool as a program for building skeletonized models of 3D structures with a graphical user interface. GUI based neuronal network model building.

Proper citation: MCTrace (RRID:SCR_016532) Copy   

•   Source: SciCrunch Registry

http://www.mediacy.com/imagepro

Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection.

Proper citation: Image Pro (RRID:SCR_016497) Copy   

•   Source: SciCrunch Registry

https://www.humancellatlas.org

Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease.

Proper citation: Human Cell Atlas (RRID:SCR_016530) Copy   

•   Source: SciCrunch Registry

https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl

Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.

Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy   

•   Source: SciCrunch Registry

http://www.broadcvdi.org/

Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.

Proper citation: Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) Copy   

•   Source: SciCrunch Registry

http://www.ajnr.org/content/25/6/945.long

Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files.

Proper citation: jPerfusionModule (RRID:SCR_016534) Copy   

•   Source: SciCrunch Registry

http://www.cyto.purdue.edu/cdroms/micro1/7_spon/vaytek/voxblast.htm

Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.

Proper citation: VoxBlast (RRID:SCR_016491) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.1016/j.neuroimage.2018.07.046

Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.

Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/homer/microarray/index.html

Software tool to analyze the promoters of genes and look for motifs that are enriched in the target gene promoters relative to other promoters. Used for gene based analysis to provide a list of genes that should contain the same elements, such as genes that are co-regulated. It includes gene ontology analysis and can be used to look for RNA motifs in mRNAs.

Proper citation: findMotif.pl (RRID:SCR_016417) Copy   

•   Source: SciCrunch Registry

https://github.com/INM-6/NetworkUnit

Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level.

Proper citation: NetworkUnit (RRID:SCR_016543) Copy   

•   Source: SciCrunch Registry

http://en.toitu.co.jp/mt-516/

Fetal actocardiograph instrument provided by TOITU CO., LTD.

Proper citation: Fetal Actocardiograph MT-516 (RRID:SCR_016420) Copy   

•   Source: SciCrunch Registry

https://omabrowser.org/oma/

Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OMA Orthology database (RRID:SCR_016425) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/HARP

Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.

Proper citation: HARP (RRID:SCR_016546) Copy   

•   Source: SciCrunch Registry

https://github.molgen.mpg.de/MPIBR-coattia/MatlabMain/tree/master/behaviorAnalysis/code/NSKtoolbox/externalToolboxes/kCSDv1

Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes.

Proper citation: kCSD-Matlab (RRID:SCR_016424) Copy   

•   Source: SciCrunch Registry

https://github.com/mpi2/vpv

Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.

Proper citation: VPV (RRID:SCR_016545) Copy   

•   Source: SciCrunch Registry

https://lifescience.bioquant.com/

Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders.

Proper citation: BIOQUANT Life Science (RRID:SCR_016423) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/danio-code/public/dcc

Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts.

Proper citation: DCC (RRID:SCR_016544) Copy   

•   Source: SciCrunch Registry

https://cm.jefferson.edu/rna22/

Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.

Proper citation: RNA22 (RRID:SCR_016507) Copy   

•   Source: SciCrunch Registry

http://cajadb.neuro.ufrn.br

Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.

Proper citation: CajaDB (RRID:SCR_016506) Copy   

•   Source: SciCrunch Registry