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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.
Proper citation: Ecosystem for Multi-modal Brain-behavior Experimentation and Research (RRID:SCR_026700) Copy
https://github.com/SynapseWeb/PyReconstruct
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.
Proper citation: PyReconstruct (RRID:SCR_027562) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MSM
Software tool for registering cortical surfaces. Capable of driving alignment using wide variety of descriptors of brain architecture, function and connectivity.
Proper citation: Multimodal Surface Matching (RRID:SCR_024929) Copy
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIRST
Software model based segmentation and registration tool. Used for segmentation of sub-cortical structures. Introduces basic segmentation and vertex analysis for detecting group differences.
Proper citation: FMRIB’s Integrated Registration and Segmentation Tool (RRID:SCR_024921) Copy
https://github.com/bmvdgeijn/WASP/
Software allele-specific pipeline for unbiased read mapping and molecular QTL discovery. Allele-specific software for robust molecular quantitative trait locus discovery.
Proper citation: WASP (RRID:SCR_025497) Copy
https://pypi.org/project/piano-integration/
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.
Proper citation: PIANO:Probabilistic Inference Autoencoder Networks for multi-Omics (RRID:SCR_027864) Copy
https://github.com/gillislab/CrossExpression
Software package to discover genes that coordinate their expression across spatially adjacent cells. Used for analysis of spatial transcriptomic data allowing in-depth analyses how genes coordinate their expression in space to perform tissue-level functions. Facilitates analysis and exploration of cross-expression patterns.
Proper citation: CrossExpression (RRID:SCR_027990) Copy
https://brain-specimenportal.org/unified_resource_browser?resource_type=donor
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.
Proper citation: NIMP Analytics (RRID:SCR_028218) Copy
https://github.com/GabrielHoffman/dreamlet
Software R package enables differential expression analysis on multi-sample single cell datasets using linear (mixed) models with precision weights.
Proper citation: dreamlet (RRID:SCR_028168) Copy
https://github.com/ericcfields/FMUT/wiki/
Software toolbox (FMUT) is an extension to David Groppe’s Mass Univariate ERP Toolbox (MUT). MUT implements t-tests for several different mass univariate approaches to the analysis of ERP data. FMUT adds to this by implementing one-way and factorial ANOVA versions of the same mass univariate approaches.
Proper citation: Factorial Mass Univariate Toolbox (RRID:SCR_028612) Copy
https://github.com/meganhuibregtse/peri-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.
Proper citation: PERI: Prospective Evaluation of Reproductive aging Indicators (RRID:SCR_028698) Copy
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