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https://github.com/ODonoghueLab/Aquaria

Web application to help biologists use 3D structures to gain insight into protein function. Used in revealing novel insights into molecular mechanisms underlying protein function in health and disease. System for incorporating 3D structures into variant analysis.

Proper citation: Aquaria (RRID:SCR_021834) Copy   

•   Source: SciCrunch Registry

https://www.microns-explorer.org/

Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons.

Proper citation: Microns Explorer (RRID:SCR_021678) Copy   

•   Source: SciCrunch Registry

http://connect-tbi.med.upenn.edu/

Portal for traumatic brain injury data. Common Data Elements (CDEs) and Unique Data Elements (UDEs) for digital neuropathological data and clinical data that will be collected in all CONNECT-TBI center projects. Goal is to establish multi-center, digital neuropathological data and clinical data reporting network with case accrual from each center project. Collected neuropathological data and clinical data available by sharing with center site investigators approved by Administrative Core and by submitting into FITBIR. Central TBI data repository by collecting digital neuropathological data and clinical data from TBI cases and normal controls at each center and posting library of their holdings.

Proper citation: Connect TBI (RRID:SCR_022009) Copy   

•   Source: SciCrunch Registry

https://github.com/benmurphybaum/StimGen

Software tool as interface for designing and presenting visual stimuli.

Proper citation: StimGen (RRID:SCR_021676) Copy   

•   Source: SciCrunch Registry

https://github.com/neuronanalyser/neuronanalyser

Software analysis toolkit for tracking blobs and extracting intensity values from imaging data, designed for use with ratiometric fluorescent sensors.

Proper citation: Neuronanalyser (RRID:SCR_022007) Copy   

•   Source: SciCrunch Registry

https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html

Software package for ZEISS light microscopy systems. Universal user interface for every imaging system from ZEISS to assist to acquire images, process images, visualize big data by GPU powered 3D engine, analyze images via Machine Learning-based tools, correlate between light-light or light-electron microscopes, store raw data in secure format locally or in the cloud., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ZEN-ZEISS Efficient Navigation (RRID:SCR_021725) Copy   

•   Source: SciCrunch Registry

https://github.com/HanLabBU/micro-control-final

Teensy microcontroller based interface for optical imaging camera control during behavioral experiments.

Proper citation: Teensy-Based Interface (RRID:SCR_021602) Copy   

•   Source: SciCrunch Registry

http://rna.informatik.uni-freiburg.de/MutaRNA/Input.jsp

Web server predicts and visualizes mutation induced structure changes of single nucleotide polymorphism in RNA sequence. This covers changes in accessibility (single strandedness) of molecule, its intra molecular base pairing potential and its base pairing probabilities. One of Freiburg RNA tools.

Proper citation: MutaRNA (RRID:SCR_021723) Copy   

•   Source: SciCrunch Registry

https://www.nature.com/articles/nprot.2014.131

Software tool calculates direction autocorrelation, plots and calculates other essential parameters to analyze cell migration in two dimensions: it displays cell trajectories individually and collectively, and it calculates average speed and mean square displacements (MSDs) to assess the area explored by cells over time.

Proper citation: DiPer (RRID:SCR_021720) Copy   

•   Source: SciCrunch Registry

https://www.cancer.gov/about-cancer/treatment/drugs

Portal to find consumer friendly information about drugs for cancer and conditions related to cancer. The list is in alphabetical order by generic name and brand name.

Proper citation: NIH NCI list of FDA approved cancer drugs (RRID:SCR_021841) Copy   

•   Source: SciCrunch Registry

http://cmpg.unibe.ch/software/BayeScan/index.html

Software tool to identify candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.

Proper citation: BayeScan (RRID:SCR_022018) Copy   

•   Source: SciCrunch Registry

https://github.com/kukionfr/VAMPIRE_open

Software tool for analysis of cell and nuclear morphology from fluorescence or bright field images. Enables profiling and classification of cells into shape modes based on equidistant points along cell and nuclear contours. Robust method to quantify cell morphological heterogeneity.

Proper citation: VAMPIRE (RRID:SCR_021721) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-biols/CIRIquant

Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events.

Proper citation: CIRIquant (RRID:SCR_021661) Copy   

•   Source: SciCrunch Registry

https://www.mirion.com/products/genie-2000-basic-spectroscopy-software

Software tool as comprehensive environment for data acquisition, display and analysis of gamma and alpha spectrometry data.

Proper citation: Genie 2000 Basic (RRID:SCR_021933) Copy   

•   Source: SciCrunch Registry

https://github.com/Murali-group/SARS-CoV-2-network-analysis

Software tool to predict human proteins that interact with SARS-CoV-2 proteins and trace provenance of predictions.

Proper citation: SARS-CoV-2 network analysis (RRID:SCR_021811) Copy   

•   Source: SciCrunch Registry

https://hackaday.io/project/181604-mri-stereoscope

Project provides miniature mirror stereoscope system for MRI-scanner. System takes advantage of commonly used display equipment, MRI head coil, and display screen. Miniature Wheatstone stereoscope is used for human neuroimaging.

Proper citation: MRI-stereoscope project (RRID:SCR_021655) Copy   

•   Source: SciCrunch Registry

https://www.ibm.com/products/spss-statistics

Software package for statistics. Used to analyze and visualize data. Extensions can be used, Python and R programming language code, to integrate with open source software. Available for Windows and Mac operating systems.Versions that were produced by SPSS Inc. before the IBM acquisition (Versions 18 and earlier) would be given origin or publisher of SPSS Inc. in Chicago. Versions that were released after the acquisition would be given origin or publisher of IBM Corp. in Armonk, NY.

Proper citation: IBM SPSS Statistics (RRID:SCR_016479) 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

https://github.com/VisionandCognition/NHP-pycortex

Software tool as adaptation for NHP brains and pipelines. Pycortex python based toolkit for surface visualization of fMRI data.

Proper citation: NHP pycortex (RRID:SCR_021815) Copy   

•   Source: SciCrunch Registry

https://www.ebi.ac.uk/eqtl

Catalog provides uniformly processed gene expression and splicing QTLs from all available public studies on human. Expression and splicing QTLs recomputed from public datasets.

Proper citation: eQTL Catalogue (RRID:SCR_021700) Copy   

•   Source: SciCrunch Registry