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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Multimodal Surface Matching Resource Report Resource Website |
Multimodal Surface Matching (RRID:SCR_024929) | MSM | software application, data processing software, image analysis software, software resource, registration software | Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity. | registering cortical surfaces, brain architecture, function and connectivity, | is a plug in for: FSL | NIMH 1U54MH091657; NIMH F30 MH097312 |
PMID:24939340 | Free, Freely available | SCR_024929 | MSM:Multimodal Surface Matching | 2026-08-03 09:38:28 | 0 | ||||||
|
FMRIB’s Integrated Registration and Segmentation Tool Resource Report Resource Website 1+ mentions |
FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) | FIRST | software application, data processing software, segmentation software, data analysis software, image analysis software, software resource, registration software | Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences. | Functional Magnetic Resonance Imaging of the Brain, segmentation, registration, volumetric segmentation, performing vertex analysis, |
is related to: Multimodal Image Segmentation Tool is a plug in for: FSL |
NCRR P41 RR14075; NINDS R01 NS052585; NCRR R01 RR16594; NIMH K08 MH01573; NIMH K01 MH01798; NIDA R01 DA017905 |
PMID:21352927 | Free, Freely available | SCR_024921 | , Functional Magnetic Resonance Imaging of the Brain's Integrated Registration and Segmentation Tool | 2026-08-03 09:38:54 | 2 | ||||||
|
WASP Resource Report Resource Website 1+ mentions |
WASP (RRID:SCR_025497) | software toolkit, software resource, source code | Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery. | molecular QTLs discovery, unbiased allele-specific read mapping and discovery, molecular QTLs, unbiased allele-specific read, mapping and discovery, | Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG006123; NIMH MH101825; NIGMS GM007197; NSF |
PMID:26366987 | Free, Available for download, Freely available, | SCR_025497 | 2026-08-03 09:39:09 | 3 | |||||||||
|
histoCAT Resource Report Resource Website 1+ mentions |
histoCAT (RRID:SCR_026499) | software toolkit, software resource, source code | Software package to visualize and analyse multiplexed image cytometry data interactively. | visualize and analyse multiplexed image, image cytometry data, interactively | NIA R01AG066027; NIMH U19MH114830 |
PMID:28783155 | Free, Available for download, Freely available | SCR_026499 | Histology Topography Cytometry Analysis Toolbox | 2026-08-03 09:38:50 | 2 | ||||||||
|
Borzoi Resource Report Resource Website 1+ mentions |
Borzoi (RRID:SCR_026619) | software toolkit, software resource, source code | Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences. | Borzoi models access, convolutional neural networks, predict RNA-seq coverage, | Common Fund of the Office of the Director ; NCI ; NHGRI ; NHLBI ; NIDA ; NIMH ; NINDS |
PMID:39779956 | Free, Available for download, Freely available | SCR_026619 | 2026-08-03 09:38:58 | 1 | |||||||||
|
Ecosystem for Multi-modal Brain-behavior Experimentation and Research Resource Report Resource Website 1+ mentions |
Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) | EMBER | data or information resource, service resource, data repository, storage service resource | BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program. | data archive, multi-modal neurophysiological data, behavioral data, Brain Behavior Quantification and Synchronization (BBQS) Program, |
is related to: Distributed Archives for Neurophysiology Data Integration is related to: Brain Observatory Storage Service and Database (BossDB) has parent organization: BRAIN Initiative has parent organization: Johns Hopkins University; Maryland; USA |
NIMH R24MH136632; NIDA R24DA064430 |
Free, Freely available | SCR_026700 | , Ecosystem for Multi-modal Brain-behavior Experimentation and Research (EMBER), EMBER Archive | 2026-08-03 09:38:54 | 6 | |||||||
|
PyReconstruct Resource Report Resource Website 1+ mentions |
PyReconstruct (RRID:SCR_027562) | software resource, software application, source code | Software successor to the Reconstruct annotation tool. PyReconstruct runs on all major operating systems, breaks through legacy RAM limitations, features intuitive and collaborative curation system, and employs flexible and dynamic approach to image registration. Used to analyze, display, and publish experimental or connectomics data. Suited for generating ground truth to implement in automated segmentation, outcomes of which can be returned to PyReconstruct for proofreading and quality control. | analyze, display, publish, experimental data, connectomics data, | NIMH R56MH139176; NSF |
PMID:40737319 | Free, Available for download, Freely available | SCR_027562 | 2026-08-03 09:39:10 | 1 | |||||||||
|
PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics Resource Report Resource Website |
PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics (RRID:SCR_027864) | PIANO | software resource, software application, source code | Software novel variational autoencoder framework for inferring integrated latent space representations for single cell transcriptomics data that uses a negative binomial generalized linear model for stronger batch correction, and code compilation for ten times faster training than existing tools. Enables superior analyses of multiple atlases, solving challenging integration tasks across sequencing platforms, development, and species, while simultaneously preserving desired biological signals. | Probabilistic Inference Autoencoder Networks, multi-Omics, variational autoencoder framework, inferring integrated latent space representations, single cell transcriptomics data, | is organization facet of: BRAIN Initiative Cell Atlas Network | NIMH UM1MH130981; NIMH DP2MH140136; NIMH 5T32MH065214 |
DOI:10.1101/2025.11.16.686778v2.full#sec-17 | Free, Available for download, Freely available | https://github.com/NingWang1729/piano | SCR_027864 | piano | 2026-08-03 09:39:35 | 0 | |||||
|
NIMP Analytics Resource Report Resource Website |
NIMP Analytics (RRID:SCR_028218) | NIMP | portal, web service, data access protocol, data or information resource, software resource, project portal | Neuroanatomy-anchored Information Management Platform for collaborative BICAN data generation developed by UTHealth Houston. Serves as metadata tracking engine to support generation, management, and sharing of brain research data. Integrates data production pipelines across brain banks, laboratories, sequencing centers, and data archives. Platform enables integrative and collaborative, consortium-scale FAIR data generation within the BICAN project. Platform is designed to manage complex dataset, including tissue samples and sequencing data, through Specimen Portal and Sequence Library Portal. Portals provide multiple types of data interfaces through dashboards, APIs, faceted queries, and batch data ingestion and exporting. | FAIR, BICAN, CUBIE, Sample Tracking, Data Ecosystem, Brain Tissue, Multi-Omics Profiling Expression Database, neuroanatomy, collaborative BICAN data generation, | is organization facet of: BRAIN Initiative Cell Atlas Network | NIMH U24MH130988 | PMID:41573954 | Free, Freely available, | https://brain-specimenportal.org | SCR_028218 | Neuroanatomy-Anchored Information Management Platform (NIMP) | 2026-08-03 09:39:28 | 0 | |||||
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dreamlet Resource Report Resource Website |
dreamlet (RRID:SCR_028168) | software toolkit, software resource, source code | Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights. | Perform differential expression analysis, multi-sample single cell datasets, linear mixed models, precision weights, | NIA R01AG067025; NIA R01AG065582; NIA R01AG050986; NIA P30AG066514; NIMH R01MH109677; NIMH R01MH125246; NIMH RF1MH128970; NIMH U01MH116442; NINDS U01NS125580 |
PMID:36993704 | Free, Available for download, Freely available | SCR_028168 | 2026-08-03 09:39:19 | 0 | |||||||||
|
PERI: Prospective Evaluation of Reproductive aging Indicators Resource Report Resource Website |
PERI: Prospective Evaluation of Reproductive aging Indicators (RRID:SCR_028698) | software toolkit, software resource, source code | Software R code to apply Stages of Reproductive Aging Workshop + 10 stages to prospectively collected vaginal bleeding data among a cohort of Black women aged 40–55 years. Used to apply STRAW+10 stages to prospectively tracked menstrual bleeding data in a longitudinal cohort study of perimenopausal women. | Stages of Reproductive Aging Workshop, perimenopausal women, prospectively tracked menstrual bleeding data, STRAW+ 10 stages, prospectively collected vaginal bleeding data, | NIMH R01MH128244; NIMH F32MH134528; NINDS T32NS096050 |
PMID:41576711 | Free, Available for download, Freely available | SCR_028698 | 2026-08-03 09:39:39 | 0 |
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