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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
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
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
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
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
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
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
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
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
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
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
https://app.terra.bio/#workspaces/pathogen-genomic-surveillance/COVID-19
Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics.
Proper citation: Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) Copy
Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting.
Proper citation: Image Quant TL (RRID:SCR_018374) Copy
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
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
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
http://pbil.univ-lyon1.fr/acuts/ACUTS.html
THIS RESOURCE IS NO LONGER IN SERVICE, Documented on August 12, 2014. Database that identifies new regulatory elements in untranslated regions of protein-coding genes (5 prime flanks, 5 prime UTRs, introns, 3 prime UTRs and 3 prime flanks). The analyses is focused on genes from metazoan species (essentially vertebrates, insects and nematodes). Information on highly conserved regions (sequences, alignments, annotations, bibliographic references) are compiled. Currently 176 out of 326 detected highly conserved regions (HCRs) have been analyzed and incorporated in the database. You can also access the list of annotated conserved elements and the list of conserved elements that remain to be processed. Their approach is based on comparative sequence analysis, for the identification of phylogenetic footprints.
Proper citation: Ancient conserved untranslated sequences (RRID:SCR_008130) Copy
http://bioinfo-out.curie.fr/ittaca/
THIS RESOURCE IS NO LONGER IN SERVICE, documented on 6/12/25. ITTACA is a database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma. ITTACA is developed by the Institut Curie Bioinformatics group and the Molecular Oncology group of UMR144 CNRS/Institut Curie. A web interface allows users to carry out different class comparison analyses, including comparison of expression distribution profiles, tests for differential expression, patient survival analyses, and users can define their own patient groups according to clinical data or gene expression levels. The different functionalities implemented in ITTACA are: - To test if one or more gene, of your choice, is differentially expressed between two groups of samples exhibiting distinct phenotypes (Student and Wilcoxon tests). - The detection of genes differentially expressed (Significance Analysis of Microarrays) between two groups of samples. - The creation of histograms which represent the expression level according to a clinical parameter for each sample. - The computation of Kaplan Meier survival curves for each group. ITTACA has been developed to be a useful tool for comparing personal results to the existing results in the field of transcriptome studies with microarrays.
Proper citation: Integrated Tumor Transcriptome Array and Clinical data Analysis (RRID:SCR_008182) Copy
http://www.bh4.org/BH4DatabasesBiodef.asp
THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 26, 2016. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Approximately 2% of newborns with hyperphenylalaninaemia are deficient in tetrahydrobiopterin. Selective screening must be performed in all instances where hyperphenylalaninaemia is detected by neonatal screening. In the last 20 years, 308 patients with tetrahydrobiopterin deficiencies have been recognized as a result of screening carried out, worldwide, in Departments of Paediatrics. Of these 308 patients, 181 suffered from 6-pyruvoyltetrahydropterin synthase deficiency, 92 from dihydropteridine reductase deficiency, 13 from pterin-4a-carbinolamine dehydratase deficiency, 12 from GTP cyclohydrolase I deficiency, and 10 are still unclassified. The BIODEF database have tabulated the most common clinical and laboratory data related to hyperphenylalaninaemia and tetrahydrobiopterin deficiencies. Additionally, there are data regarding treatment, outcome, and DNA analysis. Preliminary evaluation reveals that the degree of hyperphenylalaninaemia can vary from normal to 2500 mumol/L. Analyses of pterins in urine and measurement of dihydropteridine reductase activity from Guthrie cards are absolutely essential tests for accurate diagnosis. There is a regional (demographic) variation in the frequency of tetrahydrobiopterin deficiencies indicating the highest incidence in Saudi Arabia, probably a consequence of the high consanguinity rate.
Proper citation: International Database of Tetrahydrobiopterin Deficiencies (RRID:SCR_008171) Copy
http://www.nitrc.org/projects/jhucis_pedatlas/
Anatomical atlases constructed by Computational Anatomy of Johns Hopkins University for analysis of shape vectors. The atlases were generated from segmented hippocampal and amygdala structures in acquired populations of children, adolescents and young adults in neuroimaging studies of major depression disorder (MDD) at Washington University at St Louis.
Proper citation: Atlases of amygdala and hippocampus for pediatric populations (RRID:SCR_014085) Copy
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