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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Blue Brain Cell Atlas Resource Report Resource Website 10+ mentions |
Blue Brain Cell Atlas (RRID:SCR_019266) | data or information resource, atlas | Describes number, types, and positions of cells in all areas of mouse brain. Provides densities and positions of all excitatory, inhibitory and neuromodulatory neurons, as well as astrocytes, oligodendrocytes and microglia in each of brain regions defined in Allen Mouse Brain Atlas. Users can download cell numbers for statistical analysis, cell positions and types for modeling and visualizing brain areas. Underlying workflow uses imaging data from Allen Institute Common Coordinate Framework to generate cell positions and assign their type using API for data access. | Cell number, cell type, cell position, brain area, mouse brain, neuromodulatory neurons, astrocytes, oligodendrocytes, microglia, imaging data, Allen Institute Common Coordinate Framework |
is used by: BICCN is related to: Allen Mouse Brain Reference Atlas is related to: Allen Institute for Brain Science is provided by: Blue Brain Project |
Free, Freely available | SCR_019266 | The Blue Brain Cell Atlas | 2026-08-09 09:07:25 | 11 | |||||||||
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Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas Resource Report Resource Website 1+ mentions |
Enhanced and Unified Anatomical Labeling for Common Mouse Brain Atlas (RRID:SCR_019267) | data or information resource, atlas | Website to visualize and share anatomical labels. Franklin and Paxinos (FP) based anatomical labels in Allen Common Coordinate Framework (CCF). Cell type specific transgenic mice and MRI atlas were used to adjust and further segment labels. New segmentations were created in dorsal striatum using cortico-striatal connectivity data. Anatomical labels were digitized based on Allen ontology, and web-interface was created for easy visualization. These labels provide resource to isolate and identify mouse brain anatomical structures. Open source data sharing will facilitate further refinement of anatomical labels and integration of data interpretation within single anatomical platform. | Anatomical labels, Allen Common Coordinate Framework, Franklin and Paxinos labels, MRI atlas, segment labels, transgenic mice, dorsal striatum, cortico-striatal connectivity data, mouse brain anatomical structure |
is used by: BICCN is related to: Allen Institute for Brain Science |
NIMH R01 MH116176; NINDS R01 NS10 8407; Pennsylvania Department of Health ; NIH Office of the Director R24 OD018559 |
PMID:31699990 | Free, Freely available | SCR_019267 | 2026-08-09 09:07:50 | 2 | ||||||||
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Harvard Tissue Atlas Resource Report Resource Website 1+ mentions |
Harvard Tissue Atlas (RRID:SCR_022829) | HTA | data or information resource, atlas | Gathers together imaging and omic datasets into molecular maps of normal and diseased tissue from human and animal models, with emphasis on cancer. Used to access datasets, educational curriculum and talks, and recommended methods and software. | imaging and omic datasets, molecular maps, normal and diseased tissue, human and animal models, cancer datasets | has parent organization: Harvard University; Cambridge; United States | cancer | Free, Freely available | SCR_022829 | tissue-atlas.org | 2026-08-09 09:08:28 | 2 | |||||||
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Kidney Tissue Atlas Resource Report Resource Website 10+ mentions |
Kidney Tissue Atlas (RRID:SCR_021626) | data or information resource, atlas | Atlas is set of interactive tools built to promote retrieval, exploration, discovery, and analysis of Kidney Precision Medicine Project data by greater research community. Datasets available in repository are combination of raw and processed data from KPMP participant biopsies and reference tissue samples. | Interactive tools, retrieval, exploration, discovery, analysis, Kidney Precision Medicine Project data | is related to: Kidney Precision Medicine Project | Free, Freely available | SCR_021626 | 2026-08-09 09:08:02 | 38 | ||||||||||
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Predomics Resource Report Resource Website 1+ mentions |
Predomics (RRID:SCR_017415) | software application, source code, software resource | Software package for metagenomics data. Discovers accurate predictive signatures and provides unprecedented interpretability. Package contains three methods for suppervised learning based on ternary coefficients. Used to discover classification models for quantitative metagenomics data. | Metagenomic, data, discover, predictive, signature, unprecedented, interpretability, supervised, learning, ternary, coefficient | EU-FP7 HEALTH-F4-2012-305312; Assistance Publique-Hôpitaux de Paris Contrat d’interface chercheurs 2015-2018; French National Agency |
DOI:10.1101/409144 | Free, Available for download, Freely available | SCR_017415 | 2026-08-09 09:07:04 | 1 | |||||||||
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Tabula Sapiens Resource Report Resource Website 10+ mentions |
Tabula Sapiens (RRID:SCR_022314) | data or information resource, atlas | Single cell transcriptomic atlas of multiple organs from individual human donors. Multiple organ, single cell transcriptomic atlas of humans. Molecular reference atlas for cell types of human body. Provides molecular definition of these cell types and reveals many other aspects of human biology, including how same gene can be spliced differently in different cell types, how shared cell types in different tissues can have subtle differences in their identities, and how clones of immune system can be shared across tissues. | Single cell transcriptomic atlas, multiple organs, human donors, molecular reference atlas | diabetes, cancer, hypertension, coronary artery disease, hyperlipidemia, bipolar, depression, deep vein thrombosis, flu, mitral regurgitation, osteopenia, venous thromboembolic disease, lupus, pulmonary hypertension, schizophrehnia, seizure, asthma, atrial fibrillation, asplenia, ezcema, hypercholesterolemia, chronic lung disease | Chan Zuckerberg Initiative | DOI:10.1101/2021.07.19.452956 | Free, Freely available | SCR_022314 | 2026-08-09 09:08:21 | 43 | ||||||||
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EM-DECODER Resource Report Resource Website 1+ mentions |
EM-DECODER (RRID:SCR_000023) | EM-DECODER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A haplotype inference program. | gene, genetic, genomic |
is listed by: Genetic Analysis Software has parent organization: Harvard University; Cambridge; United States |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154297 | SCR_000023 | 2026-08-09 09:02:53 | 1 | ||||||||
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4Peaks Resource Report Resource Website 10+ mentions |
4Peaks (RRID:SCR_000015) | 4Peaks | software application, software resource | Software application for viewing and editing sequence trace files. | mac os x, sequence, trace file | is listed by: OMICtools | Free | OMICS_01015 | SCR_000015 | 2026-08-09 09:02:53 | 15 | ||||||||
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Seattle Alzheimer Disease Brain Cell Atlas Resource Report Resource Website 10+ mentions |
Seattle Alzheimer Disease Brain Cell Atlas (RRID:SCR_023110) | SEA-AD | data or information resource, atlas | Open atlas based on single cell profiling technologies with quantitative neuropathology and deep clinical phenotyping from middle temporal gyrus from neurotypical reference brains and brains from SEA-AD aged cohort that span spectrum of Alzheimer’s disease. Produced via collaboration between Allen Institute for Brain Science, University of Washington Alzheimer Disease Research Center and Kaiser Permanente Washington Health Research Institute. | Alzheimer’s disease, single cell profiling, quantitative neuropathology, deep clinical phenotyping, middle temporal gyrus, neurotypical reference brains, SEA-AD aged cohort brains, |
is related to: BRAIN Initiative is related to: Allen Institute for Brain Science is related to: University of Washington; Seattle; USA |
Alzheimer’s disease | NIA U19AG060909 | Free, Freely available | SCR_023110 | 2026-08-09 09:08:31 | 17 | |||||||
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Pancreatlas Resource Report Resource Website 10+ mentions |
Pancreatlas (RRID:SCR_018567) | data or information resource, atlas | Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families. | Human pancreas data, pancreas image, reference dataset, human pancreas sample, organ donor pancreas data |
lists: Exeter Archival Diabetes Biobank (EADB) is related to: Vanderbilt University; Tennessee; USA is related to: Human Islet Research Network (HIRN) works with: Exeter Archival Diabetes Biobank (EADB) |
Type 1 diabetes, Diabetes, Type 2 diabetes, Cystic Fibrosis-Related Diabetes | Leona M. and Harry B. Helmsley Charitable Trust ; NIDDK DK104211; NIDDK DK108120; NIDDK DK112232; NIDDK DK106755; NIDDK DK20593; NCI CA68485; NIDDK DK58404; NIDDK DK59637; NEI EY08126 |
Free, Freely available | SCR_018567 | 2026-08-09 09:07:43 | 13 | ||||||||
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Allen Brain Atlas expression map of Cre and other drivers Resource Report Resource Website 1+ mentions |
Allen Brain Atlas expression map of Cre and other drivers (RRID:SCR_017510) | data or information resource, atlas | Data detailing transgene expression in Cre and other driver lines for adult and developing brain. Experiments include colorimetric in situ hybridization, fluorescent in situ hybridization and other histological methods. Expression maps of transgenic Cre and other driver lines in mice. | Data, image, transgene, expression, Cre, brain, map, mice | has parent organization: Allen Brain Atlas | Free, Freely available | SCR_017510 | Allen Brain Atlas Data Portal Transgenic Characterization | 2026-08-09 09:07:05 | 9 | |||||||||
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White Adipose Atlas Resource Report Resource Website 1+ mentions |
White Adipose Atlas (RRID:SCR_023625) | data or information resource, atlas | Single cell atlas of human and mouse white adipose tissue. | white adipose tissue, adipose tissue, human, mouse | NIDDK RC2 DK116691; NIDDK 5P30 DK057521; NIDDK F32 DK124914; Italian Ministry of University ; Novo Nordisk Foundation ; Lundbeck Foundation ; NIDDK UM1 DK126185; Sarnoff Cardiovascular Research Foundation Fellowship ; NHGRI 1K08 HG010155; NHGRI 1U01 HG011719; NIDDK P30 DK046200 |
PMID:35296864 | Free, Freely available | SCR_023625 | 2026-08-09 09:08:17 | 8 | |||||||||
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Common Metabolic Disease Genome Atlas Resource Report Resource Website 1+ mentions |
Common Metabolic Disease Genome Atlas (RRID:SCR_022983) | CMDGA | data or information resource, atlas | Component of Accelerating Medicines Partnership Common Metabolic Diseases being developed at University of California San Diego as part of larger consortium of academic, industry and non-profit institutions worldwide. Resource is based on software developed by ENCODE DCC at Stanford University. Atlas provides epigenomics and other functional genomics data to promote understanding of genetic basis of common metabolic diseases. | AMP-CMD, Accelerating Medicines Partnership, Common Metabolic Diseases, epigenomics, functional genomics data, metabolic diseases |
is related to: Common Metabolic Diseases Knowledge Portal is related to: University of California at San Diego; California; USA |
metabolic diseases | Free, Freely available | SCR_022983 | 2026-08-09 09:08:10 | 9 | ||||||||
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Brain Injury Knowledge Ontology Resource Report Resource Website |
Brain Injury Knowledge Ontology (RRID:SCR_024628) | BIKO | data or information resource, controlled vocabulary, ontology | Application ontology to formalize concepts and methods used in translational traumatic brain injury research. Multi species translational traumatic brain injury ontology to assist in formalizing concepts and methods used in traumatic brain injury research. | Multi species translational traumatic brain injury ontology, translational traumatic brain injury ontology, traumatic brain injury, | Free, Freely available | SCR_024628 | , BIKO-TBI, BIKO Traumatic Brain Injury, Brain Injury Knowledge Ontology Traumatic Brain Injury, BIKO TBI | 2026-08-09 09:09:05 | 0 | |||||||||
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UManitoba - JHU Functionally Defined Human White Matter Atlas Resource Report Resource Website 1+ mentions |
UManitoba - JHU Functionally Defined Human White Matter Atlas (RRID:SCR_015525) | data or information resource, atlas | Probabilistic atlas of human white matter tracts/regions underlying several well-known resting state brain networks. The atlas includes group probability maps for each network, as well as each individual tract that are aligned to both the SPM and MRIStudio ICBM templates. | white matter, dti tractography, resting state brain network, group probability map |
works with: MRI Studio works with: SPM works with: 3D Slicer |
PMID:26578930 | Acknowledgement requested, Freely available, Available for download | SCR_015525 | UManitoba JHU Functionally Defined Human White Matter Atlas, UManitoba-JHU Functionally-Defined Human White Matter Atlas | 2026-08-09 09:06:41 | 1 | ||||||||
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Brain Maps Resource Report Resource Website 1+ mentions |
Brain Maps (RRID:SCR_017314) | data or information resource, atlas | Atlas with global nervous system nomenclature ontology and flatmaps for structure of rat brain. Open access resource for neuroscience community. | atlas, nervous, system, nomenclature, ontology, flatmap, structure, brain, rat | PMID:29277900 | Free, Freely available | SCR_017314 | Brain maps 4.0, Brain maps | 2026-08-09 09:07:14 | 5 | |||||||||
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LifeLegacy Foundation Resource Report Resource Website 1+ mentions |
LifeLegacy Foundation (RRID:SCR_000518) | material resource, biomaterial supply resource | A non-profit tissue bank that facilitates the distribution of non-transplantable tissue to the medical and research community. It provides snap frozen low post mortem interval (PMI) tissue, normal and diseased tissue, plastinated specimens, anatomical specimens, and specialty specimens. The foundation also works to increase public awareness of research tissue donation for medical research. | tissue, bank, medicine, research, body, transplant, biomaterial | is listed by: One Mind Biospecimen Bank Listing | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_37185 | SCR_000518 | LifeLegacy | 2026-08-09 09:02:59 | 1 | ||||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software toolkit, software resource | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-08-09 09:02:57 | 31 | ||||||||
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Acquisition and Analysis for Electron Tomography Resource Report Resource Website |
Acquisition and Analysis for Electron Tomography (RRID:SCR_000192) | TOM Toolbox | software toolkit, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software platform for low dose electron tomography (ET) for all processing steps: acquisition, alignment, reconstruction, and analysis. Requires: Matlab R2008a and Image Processing Toolbox (V6.1) | electron microscope, electron tomography, acquisition, alignment, analysis, processing, reconstruction, software, alignment, reconstruction, processing | has parent organization: Max Planck Institute of Biochemistry; Martinsried; Germany | PMID:15721576 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-10145 | http://www.biochem.mpg.de/en/rd/baumeister/tom_e/ | SCR_000192 | TOM software toolbox | 2026-08-09 09:02:55 | 0 | |||||
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DicomWorks Resource Report Resource Website 1+ mentions |
DicomWorks (RRID:SCR_001195) | DicomWorks | software application, software resource | Software to help users work with DICOM files by organizing, managing and analyzing them. Key features: * a smart DICOM viewer with 4 panel display, annotations, arrows, multimodality synchronization, etc... * an export wizard to the most common picture or movie file formats * an export wizard to Microsoft PowerPoint * the most simple and compatible DICOM CD-ROM reader * the most simple and smart DICOM CD-ROM WRITER * an archiving solution with lossless compression of the data * a DICOM creation module to dicomize images from any image source (even video capture) * e-mail or FTP import end export functions (teleradiology) * 16 native localized versions | dicom, windows, radiology, image analysis, anonymization, protocol, export, powerpoint, surface analysis, visualization | is listed by: Biositemaps | PMID:17333414 PMID:18003565 |
Free | nif-0000-00288 | http://www.dicomworks.com | SCR_001195 | 2026-08-09 09:03:07 | 3 |
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