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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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INIA19 Primate Brain Atlas Resource Report Resource Website 1+ mentions |
INIA19 Primate Brain Atlas (RRID:SCR_009498) | INIA19 Primate Brain Atlas | data or information resource, atlas, reference atlas | Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas. | atlas data, magnetic resonance, nifti, neuromaps, brain atlas, mri, minimum-deformation template |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: BrainInfo has parent organization: Integrative Neuroscience Initiative on Alcoholism |
PMID:23230398 | Creative Commons Attribution License | nlx_155646 | SCR_009498 | 2026-08-09 09:05:03 | 4 | |||||||
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resting-state pediatric imaging template Resource Report Resource Website |
resting-state pediatric imaging template (RRID:SCR_009647) | resting-state pediatric imaging template | data or information resource, atlas, reference atlas | Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates. | analyze, atlas data, magnetic resonance, child, resting-state, pediatric, adolescent | is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) | Public Domain | nlx_155978 | SCR_009647 | 2026-08-09 09:05:26 | 0 | ||||||||
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ICBM 152 Nonlinear atlases version 2009 Resource Report Resource Website 100+ mentions |
ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) | data or information resource, atlas, reference atlas | Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information. | magnetic resonance imaging, brain, human, normal |
is related to: MINC/Atlases is related to: bic-mni-models has parent organization: McConnell Brain Imaging Center |
nlx_144297 | SCR_008796 | , BIC ICBM 152 Nonlinear atlases version 2009 | 2026-08-09 09:05:02 | 278 | |||||||||
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NIHPD Objective 1 atlases (4.5 - 18.5y) Resource Report Resource Website 10+ mentions |
NIHPD Objective 1 atlases (4.5 - 18.5y) (RRID:SCR_008794) | NIHPD Objective 1 atlases (4.518.5y) | data or information resource, atlas, reference atlas | An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask. | pediatric, human, mri, brain, child, young human | has parent organization: McConnell Brain Imaging Center | Normal brain development, Aging | PMID:20656036 | nlx_144295 | SCR_008794 | BIC NIHPD Objective 1 atlases (4.518.5y), McConnell Brain Imaging Center NIHPD Objective 1 atlases (4.518.5y) | 2026-08-09 09:04:53 | 11 | ||||||
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IBDREG Resource Report Resource Website |
IBDREG (RRID:SCR_013127) | software application, software resource | Software package in S-PLUS and R to test genetic linkage with covariates by regression methods with response IBD sharing for relative pairs. Account for correlations of IBD statistics and covariates for relative pairs within the same pedigree. (entry from Genetic Analysis Software) | gene, genetic, genomic, r/s-plus | is listed by: Genetic Analysis Software | nlx_154588, SCR_009366, nlx_154407 | http://mayoresearch.mayo.edu/mayo/research/schaid_lab/software.cfm | SCR_013127 | R/IBDREG | 2026-08-09 09:06:13 | 0 | ||||||||
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GenBiomApps Resource Report Resource Website 1+ mentions |
GenBiomApps (RRID:SCR_025542) | software toolkit, software resource | Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures. | Clopper-Pearson Confidence Interval, Generalized Binomial Distribution, distribution function, quantile function, random generation | Free, Available for download, Freely available | SCR_025542 | 2026-08-09 09:09:17 | 1 | |||||||||||
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km.ci Resource Report Resource Website |
km.ci (RRID:SCR_025543) | software toolkit, software resource | Software R package to compute various confidence intervals for the Kaplan-Meier estimator, namely: Peto's CI, Rothman CI, CI's based on Greenwood's variance, Thomas and Grunkemeier CI and the simultaneous confidence bands by Nair and Hall and Wellner. | Confidence intervals, Kaplan-Meier estimator, | Free, Available for download, Freely available | SCR_025543 | 2026-08-09 09:08:46 | 0 | |||||||||||
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3D Developmental Mouse Brain Common Coordinate Framework Resource Report Resource Website 1+ mentions |
3D Developmental Mouse Brain Common Coordinate Framework (RRID:SCR_025544) | data or information resource, atlas | Open access multimodal 3D atlases of developing mouse brain that can be used to integrate mouse brain imaging data for visualization, education, cell census mapping, and more. Atlas ages include E11.5, E13.5, E15.5, E18.5, P4, P14, and P56. Web platform can be utilized to visualize and explore the atlas in 3D. Downloadable atlas can be used to align multimodal mouse brain data. Morphologically averaged symmetric template brains serve as the basis reference space and coordinate system. Anatomical labels are manually drawn in 3D based on the prosomeric model. For additional references, the P56 template includes templates and annotations from the aligned Allen Mouse Brain Common Coordinate Framework (Allen CCFv3) and aligned Molecular Atlas of the Adult Mouse Brain. | multimodal 3D atlases, developing mouse brain, mouse brain data, |
is related to: Allen Mouse Brain Common Coordinate Framework is organization facet of: BRAIN Initiative |
NIMH RF1MH12460501; NINDS R01NS108407; NIMH R01MH116176; NIBIB R01EB031722 |
PMID:37745386 | Free, Freely available | SCR_025544 | DevCCF | 2026-08-09 09:09:15 | 2 | |||||||
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pbmm2 Resource Report Resource Website 1+ mentions |
pbmm2 (RRID:SCR_025549) | source code, software resource | Software application as minimap2 frontend for PacBio native data formats. SMRT C++ wrapper for minimap2's C API. | minimap2, PacBio, native data formats, SMRT C++ wrapper, minimap2 C API, | Free, Available for download, Freely available, | SCR_025549 | 2026-08-09 09:09:17 | 7 | |||||||||||
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signed ks test Resource Report Resource Website 1+ mentions |
signed ks test (RRID:SCR_025636) | source code, software resource | Software tool as modified R ks.test to obtain sign and force exact p-value. | modified R ks.test, obtain sign and force exact p-value, p-value, | Free, Available for download, Freely available, | SCR_025636 | 2026-08-09 09:08:49 | 1 | |||||||||||
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2s-LCA Resource Report Resource Website 1+ mentions |
2s-LCA (RRID:SCR_025613) | software application, software resource | Software for multi-omic data integration. Used to jointly decompose multiple biologically related experimental data sets with biological and technological relationships that can be structured into the decomposition. | multi-omic data integration, two-stage linked component analysis, jointly decompose biologically related experimental data sets, decomposition, | PMID:35358296 | https://github.com/CHuanSite/SJD | SCR_025613 | two-stage Linked Component Analysis | 2026-08-09 09:08:48 | 1 | |||||||||
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GRNBoost2 Resource Report Resource Website 10+ mentions |
GRNBoost2 (RRID:SCR_025614) | software application, software resource | Algorithm for regulatory network inference using gradient boosting, based on GENIE3 architecture. Used for inference of gene regulatory networks. | GRN, Gene Regulatory Network, inference of gene regulatory networks, | PMID:30445495 | Free, Freely available | https://arboreto.readthedocs.io/en/latest/, https://github.com/aertslab/GRNBoost | SCR_025614 | GRNBoost, Gene Regulatory Network Boost | 2026-08-09 09:09:17 | 11 | ||||||||
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Cloud-SPAN Resource Report Resource Website 1+ mentions |
Cloud-SPAN (RRID:SCR_025594) | software application, software resource | Cloud-based high performance computing for specialised analyses on environmental omics. | specialised analyses, environmental omics, | Free, Freely available, | SCR_025594 | Cloud SPecialised ANalyses | 2026-08-09 09:09:16 | 1 | ||||||||||
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ISOLDE Resource Report Resource Website 10+ mentions |
ISOLDE (RRID:SCR_025577) | software application, software resource | Software environment to ease task of building macromolecular models into low to medium resolution experimental maps. Physically realistic environment for model building into low-resolution electron-density maps. Can generate maps directly from crystallographic F/sigF data in MTZ format and automatically re-calculate them when model changes, and/or generate "static" maps from pre-calculated F/phi data. | software environment, model building, building macromolecular models, low resolution electron density maps, experimental maps, | is a plug in for: UCSF ChimeraX | Wellcome Trust | PMID:29872003 | Free, Freely available | SCR_025577 | 2026-08-09 09:08:47 | 13 | ||||||||
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Automated Systematic Search Deduplicator Resource Report Resource Website 1+ mentions |
Automated Systematic Search Deduplicator (RRID:SCR_025607) | ASySD | software application, software resource | Open source, interoperable software tool to remove duplicate citations in biomedical systematic reviews. | automated deduplication, systematic searches, biomedical reviews, | has parent organization: University of Edinburgh; Scotland; United Kingdom | European Union’s Horizon 2020 ; Alzheimer Research UK Pilot Grant ; Stroke Association |
PMID:37674179 | Free, Freely available | SCR_025607 | Automated Systematic Search Deduplicator:ASySD | 2026-08-09 09:08:48 | 2 | ||||||
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Invicro Vivoquant Resource Report Resource Website 1+ mentions |
Invicro Vivoquant (RRID:SCR_025778) | software application, software resource | Software multi-modality post-processing suite for SPECT, CT, PET, MR, Optical and and Autoradiography imaging data. | preclincial imaging, imaging data processing, | Restricted | SCR_025778 | Vivoquant | 2026-08-09 09:09:19 | 6 | ||||||||||
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EuCanImage FHIR ETL Implementation Resource Report Resource Website 1+ mentions |
EuCanImage FHIR ETL Implementation (RRID:SCR_025824) | source code, software resource | Software application as ETL implementation for EuCanImage, encouraging semantic interoperability of clinical data obtained in studies by transforming it into machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create dictionaries following FHIR compliant structure. Code Language is written in Python 3.11. Outputs are JSON files compliant with FHIR 4.3 schemas.This script is specifically created for the Extract, Transform and Load implementation for EuCanImage, and will follow the structures obtained from the REDCap databases within the study. | FHIR, ETL, EGA, semantic interoperability of clinical data, FHIR standard, FHIR compliant structure, | European Union's Horizon 2020 research and innovation programme 952103 | DOI:10.1101/2024.03.15.24303032 | Free, Available for download, Freely available | https://workflowhub.eu/collections/25 | SCR_025824 | 2026-08-09 09:09:20 | 1 | ||||||||
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SEER*Stat Resource Report Resource Website 100+ mentions |
SEER*Stat (RRID:SCR_025808) | software application, software resource | Statistical software for analysis of SEER and other cancer-related databases.Used to view individual cancer records and to produce statistics for studying impact of cancer on population. | Statistics, analysis of SEER data, cancer records, |
is listed by: SEER Datasets and Software is related to: Surveillance Epidemiology and End Results works with: ProjPrev |
Restricted | https://seer.cancer.gov/seerstat/download/ | SCR_025808 | 2026-08-09 09:09:19 | 146 | |||||||||
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Bruker OPUS Resource Report Resource Website 10+ mentions |
Bruker OPUS (RRID:SCR_025806) | software application, software resource | Software developed by Bruker for analysis and processing of spectroscopic data. Used for measurement, processing and evaluation of IR, NIR and Raman spectra. | Bruker, spectroscopic data, measurement, processing, evaluation, IR, NIR, Raman, spectra | Restricted | https://www.bruker.com/en/products-and-solutions/infrared-and-raman/opus-spectroscopy-software/downloads.html | SCR_025806 | OPUS 8.2, OPUS | 2026-08-09 09:09:20 | 30 | |||||||||
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Ratan-lab (SUMO) Resource Report Resource Website 10+ mentions |
Ratan-lab (SUMO) (RRID:SCR_025687) | SUMO | source code, software resource | Software for multiomic nonnegative matrix factorization. | multiomic nonnegative matrix factorization, matrix factorization | DOI:10.1016/j.crmeth.2021.100152 | Free, Available for download, Freely available, | SCR_025687 | 2026-08-09 09:08:50 | 42 |
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