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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ImageQuant (RRID:SCR_014246) Copy
https://pathcore.bsd.uchicago.edu/Downloads/HTRC_ImageScUG.pdf
Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: ImageScope (RRID:SCR_014311) Copy
http://www.usadellab.org/cms/index.php?page=trimmomatic
Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows.
Proper citation: Trimmomatic (RRID:SCR_011848) Copy
Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems.
Proper citation: ProteinLynx Global Server (RRID:SCR_016664) Copy
http://www.cb.uu.se/~amin/BlobFinder/
Software that can perform calculations on cells from fluorescence microscopy images. BlobFinder can perform two types of analysis: an average count analysis to count the number of fluorescent signals and nuclei in an image, and a single cell analysis to simulate a cytoplasm and assign each signal to a particular cell.
Proper citation: BlobFinder (RRID:SCR_015788) Copy
https://www.embl-hamburg.de/biosaxs/software.html
Software toolkit for small-angle scattering data analysis from biological macromolecules.
Proper citation: ATSAS (RRID:SCR_015648) Copy
https://www.phenix-online.org/documentation/reference/refinement.html
Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB.
Proper citation: Phenix.refine (RRID:SCR_016736) Copy
https://www.indicalab.com/halo/
Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.
Proper citation: HALO (RRID:SCR_018350) Copy
http://srv00.recas.ba.infn.it/ASPicDB/
A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.
Proper citation: ASPicDB (RRID:SCR_002102) Copy
http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html
V3D is a handy, fast, and versatile 3D/4D/5D Image Visualization & Analysis System for Bioimages & Surface Objects. It also provides many unique functions, is Open Source, supports a very simple and powerful plugin interface and thus can be extended & enhanced easily. V3D-Neuron is a powerful 3D neuron reconstruction, visualization, and editing software built on top of V3D. Both V3D and V3D-Neuron have recently been published in Nature Biotechnology (April, 2010), and Highlighted in Nature Methods (May, 2010), and Science News (April, 2010), etc. V3D is a cross-platform (Mac, Linux, and Windows) tool for visualizing large-scale (gigabytes, and 64-bit data) 3D image stacks and various surface data. It is also a container of powerful modules for 3D image analysis (cell segmentation, neuron tracing, brain registration, annotation, quantitative measurement and statistics, etc) and data management. This makes V3D suitable for various bioimage informatics applications, and a nice platform to develop new 3D image analysis algorithms for high-throughput processing. In short, V3D streamlines the workflow of visualization-assisted analysis. In the latest V3D development, it can render 5D (spatial-temporal) data directly in 3D volume-rendering mode; it supports convenient and interactive local and global 3D views at different scales. It even has a Matlab file IO toolbox. A user can now write his/her own plugins to take advantage of the V3D platform very easily.
Proper citation: V3D (RRID:SCR_008646) Copy
http://www.ebi.ac.uk/Tools/sss/fasta/
Software package for DNA and protein sequence alignment to find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence.
Proper citation: FASTA (RRID:SCR_011819) Copy
Dataset of cellular signatures that catalogs transcriptional responses of human cells to chemical and genetic perturbation. CMap contains perturbagens, expression signatures, and small molecules from cell lines.
Proper citation: CMap (RRID:SCR_016204) Copy
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
Proper citation: DESeq2 (RRID:SCR_015687) Copy
http://accelrys.com/products/collaborative-science/biovia-pipeline-pilot/
Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results.
Proper citation: Pipeline Pilot (RRID:SCR_014917) Copy
https://www.rdocumentation.org/packages/pheatmap/versions/0.2/topics/pheatmap
Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters.
Proper citation: pheatmap (RRID:SCR_016418) Copy
http://www.repeatmasker.org/RepeatModeler/
Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RepeatModeler (RRID:SCR_015027) Copy
https://www.openepi.com/Menu/OE_Menu.htm
Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection.
Proper citation: OpenEpi (RRID:SCR_021913) Copy
Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version.
Proper citation: Epi Info (RRID:SCR_021682) Copy
https://business-lounge.heidelbergengineering.com/de/de/products/heidelberg-eye-explorer/
Platform that centralizes management of ophthalmic images. HEYEX interfaces with electronic medical record systems and third-party devices to allow exchange, storage, and dynamic review of diagnostic images. Heidelberg Engineering imaging products use Heidelberg Eye Explorer software platform and database to store patient information and images.
Proper citation: Heidelberg Eye Explorer (RRID:SCR_022045) Copy
http://www.mathworks.com/products/matlab/
Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance.
Proper citation: MATLAB (RRID:SCR_001622) Copy
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