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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | data analysis software, data processing software, image analysis software, software application, software resource | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-08-29 11:25:39 | 16 | |||||||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | alignment software, data processing software, image analysis software, software application, software resource | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | AMEDD Advanced Medical Technology Initiative ; NHLBI U54 HL127624; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-08-29 11:25:16 | 1 | ||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | data analysis software, data processing software, software application, software resource, software toolkit | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-08-29 11:25:40 | 1 | ||||||
|
LungMap Resource Report Resource Website 50+ mentions |
LungMap (RRID:SCR_016347) | LungMAP | data or information resource, data repository, portal, service resource, storage service resource | Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool. | lung, data, histochemistry, structural, molecular, normal, perinatal, postnatal, development, mouse, human, repository, images, transcriptomic, proteomic, lipidomic |
is related to: RTI International is related to: University of Texas at Austin; Texas; USA is related to: University of Alabama at Birmingham; Alabama; USA is related to: Yale University; Connecticut; USA is related to: University of California at San Diego; California; USA is related to: Carnegie Mellon University; Pennsylvania; USA is related to: Lung Genome Browser |
the National Heart ; Lung ; and Blood Institute of the National Institutes of Health U01HL122638 |
PMID:28798251 | Free, Freely available | SCR_016347 | The Molecular Atlas of Lung Development Program | 2026-08-29 11:25:12 | 68 | ||||||
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Lifebit Deploit Resource Report Resource Website 1+ mentions |
Lifebit Deploit (RRID:SCR_016428) | analysis service resource, data analysis service, data management software, production service resource, service resource, software application, software resource | Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines. | Lifebit, compute, management, data, analysis, cloud, integrate, data, reproduce, transparent, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28398311 | Commercially available | biotools:nextflow | https://bio.tools/nextflow | SCR_016428 | 2026-08-29 11:25:17 | 2 | |||||||
|
Ximmer Resource Report Resource Website 1+ mentions |
Ximmer (RRID:SCR_016427) | data analysis software, data processing software, data visualization software, simulation software, software application, software resource | Software to help users of targeted high throughput genomic sequencing data to accurately detect copy number variants (CNVs). Framework for running and evaluating other copy number detection tools.Used for evaluating and improving performance of CNV detection in exome and targeted sequencing data. | cnv, copy, number, variant, exome, targeted, sequencing, data, next, generation, genomic | is listed by: OMICtools | Australian National Health and Medical Research Council ; National Eye Institute ; National Heart Lung and Blood Institute ; National Human Genome Research Institute ; Victorian State Government |
DOI:10.1101/260927 | Open source, Free, Available for download, Freely available | https://omictools.com/ximmer-tool, http://ximmer.org | SCR_016427 | 2026-08-29 11:25:14 | 4 | |||||||
|
FCS Express Resource Report Resource Website 500+ mentions |
FCS Express (RRID:SCR_016431) | data analysis software, data processing software, software application, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-08-29 11:25:44 | 518 | ||||||||||
|
iMITS Resource Report Resource Website |
iMITS (RRID:SCR_016552) | iMITS | catalog, data or information resource, database | This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products. | international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPC |
is affiliated with: International Mouse Phenotyping Consortium (IMPC) is related to: GenTaR |
European Union 223592; NIH KOMP2 |
Restricted | SCR_016552 | international Micro Injection Tracking System | 2026-08-29 11:25:17 | 0 | |||||||
|
Suite2P Resource Report Resource Website 50+ mentions |
Suite2P (RRID:SCR_016434) | data analysis software, data processing software, image processing software, software application, software resource, software toolkit | Software package for processing two-photon recordings. Available together with a graphical user interface that allows manual curation of the results. Used in two-photon microscopy for the analysis of data from two-photon imaging. Registers raw movies, detects active cells, extracts their calcium traces and infers their spike times. | two, photon, microscopy, processing, image, data, record |
is related to: MATLAB has parent organization: University College London; London; United Kingdom |
Free, Available for download, Freely available | SCR_016434 | 2026-08-29 11:25:44 | 84 | ||||||||||
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | data analysis software, data analytics software, data processing software, software application, software resource | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI R01 HL105433; NHLBI U01 HL110964; NHLBI U01 HL122642 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-08-29 11:25:17 | 5 | ||||||
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Microscopy Image Browser Resource Report Resource Website 100+ mentions |
Microscopy Image Browser (RRID:SCR_016560) | MIB | data analysis software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | Software package for advanced image processing, analysis, segmentation and visualization of multi-dimensional (2D-4D) light and electron microscopy datasets. | segmentation, analysis, multidimentional, dataset, light, electron, microscopy, image, processing, visualization, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: MATLAB |
Biocenter Finland ; Biological Imaging Network Academy of Finland ; University of Helsinki |
PMID:26727152 | Free, Available for download, Freely available | biotools:mib | https://www.youtube.com/watch?v=I9FWmJX_nl0&index=1&list=PLGkFvW985wz8cj8CWmXOFkXpvoX_HwXzj, https://bio.tools/mib | SCR_016560 | MIB, Microscopy Image Browser | 2026-08-29 11:25:17 | 160 | ||||
|
MotionCor2 Resource Report Resource Website 100+ mentions |
MotionCor2 (RRID:SCR_016499) | data analysis software, data processing software, software application, software resource | 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. | anisotropic, correction, beam, induced, motion, cryo, electron, microscopy, exposure, data | has parent organization: University of California at San Francisco; California; USA | NIGMS P01 GM111126; NIH R01 GM031627 |
PMID:28250466 | Restricted | http://msg.ucsf.edu/em/software/motioncor2.html | SCR_016499 | MotionCor | 2026-08-29 11:25:15 | 186 | ||||||
|
Image Pro Resource Report Resource Website 500+ mentions |
Image Pro (RRID:SCR_016497) | data processing software, image analysis software, image processing software, software application, software resource | Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection. | MediaCybernetics Inc., capture, process, measure, analyze, share, image, data, automate, collect | Restricted | SCR_016758 | https://mediacy.com/image-pro | SCR_016497 | Image-Pro, Image-Pro Premier, Image Pro Premier | 2026-08-29 11:25:47 | 548 | ||||||||
|
Human Cell Atlas Resource Report Resource Website 100+ mentions |
Human Cell Atlas (RRID:SCR_016530) | atlas, catalog, data or information resource, database, image, map, portal | 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. | human, cell, line, atlas, catalog, map, open, data, international, project, FASEB list |
is listed by: NIDDK Information Network (dkNET) is related to: Optimus Pipeline is related to: Smart-seq2 Multi-Sample Pipeline is related to: Broad Institute Genomics Platform |
PMID:29206104 | Free, Available for download, Freely available | SCR_016530 | 2026-08-29 11:25:16 | 127 | |||||||||
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Cardiovascular Disease Knowledge Portal Resource Report Resource Website 10+ mentions |
Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) | data or information resource, database, disease-related portal, portal, topical portal | 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. | genetic, data, cardiovascular, disease, human | is listed by: NIDDK Information Network (dkNET) | cardiovascular disease, myocardial infarction, atrial fibrillation | Accelerating Medicines Partnership in Type 2 Diabetes ; National Institute of Cardiovascular Diseases and Stroke |
Free, Available for download, Google ID required, Tutorial available | SCR_016536 | 2026-08-29 11:25:16 | 31 | ||||||||
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VoxBlast Resource Report Resource Website 1+ mentions |
VoxBlast (RRID:SCR_016491) | 3d visualization software, data processing software, data visualization software, image processing software, software application, software resource | 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. | VayTek Inc., 3D, image, data, visualisation, reconstruction, measurement, projection, science, medicine |
is listed by: OMICtools has parent organization: University of Iowa Labs and Facilities |
Commercially available, Free demo version available | SCR_016491 | 2026-08-29 11:25:46 | 1 | ||||||||||
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OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | data access protocol, data or information resource, database, software application, software resource, standalone software, web service | 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. | interface, orthology, prediction, inference, complete, genome, species, data | Bayer Crop Science NV ; Swiss Institute of Bioinformatics ; UK Biotechnology and Biological Sciences Research Council ; University College London |
PMID:29106550 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016425 | Orthologous MAtrix | 2026-08-29 11:25:43 | 9 | |||||||
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HARP Resource Report Resource Website 1+ mentions |
HARP (RRID:SCR_016546) | 3d visualization software, data processing software, data visualization software, image processing software, software application, software resource, standalone software | 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. | MRC Harwell UK, automating, processing, uCT, OPT, image, data | is related to: International Mouse Phenotyping Consortium (IMPC) | Free, Available for download, Freely available | harp.exe | SCR_016546 | 2026-08-29 11:25:49 | 1 | |||||||||
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kCSD-Matlab Resource Report Resource Website 1+ mentions |
kCSD-Matlab (RRID:SCR_016424) | kCSD | data analysis software, data processing software, software application, software resource | 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. | analyzing, recording, data, multielectrode, transmembrane, current, source, estimate, kernel, source, density, method | is related to: MATLAB | Free, Available for download, Freely available | SCR_016424 | kernel Current Source Density | 2026-08-29 11:25:13 | 3 | ||||||||
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BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | 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. | BioQuant Inc., collect, analyse, data, tissue, slide, well, plate, capture, camera, scanned, image, immunofluorescence, immunohistochemistry, stereology, densitometry, 3D modeling | Commercially available, Tutoring available | SCR_016423 | 2026-08-29 11:25:43 | 20 |
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