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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-08-21 12:40:45 | 1 | ||||||
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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 | 2026-08-21 12:41:03 | 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 | 2026-08-21 12:41:04 | 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 | 2026-08-21 12:40:49 | 4 | |||||||
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Canadian Open Neuroscience Platform Resource Report Resource Website 10+ mentions |
Canadian Open Neuroscience Platform (RRID:SCR_016433) | CONP | data or information resource, data repository, organization portal, portal, service resource, storage service resource | Web interface that facilitates open science for neuroscience community by simplifying global access to and sharing of datasets and tools. Portal internalizes typical data cycle of research project, beginning with data acquisition, followed by data processing with published tools, and ultimately publication of results with link to original dataset. Platform to form interactive network of collaborations in brain research, interdisciplinary student training, international partnerships, clinical translation and open publishing. Provides unified interface to Canadian neuroscience research community. Open neuroscience research with sharing of both data and methods, to create large-scale databases, development of standards for sharing, facilitation of advanced analytic strategies, open dissemination to global community of neuroscience data and methods, and establishment of training programs for next generation of computational neuroscience researchers. | interactive, network, brain, research, interdisciplinary, student, training, international, partnership, clinical, translation, open, publishing, Canada |
is related to: Brain Canada is related to: Health Canada |
Open source | r3d100013461 | https://github.com/CONP-PCNO/conp-portal, https://doi.org/10.17616/R31NJMVP | SCR_016433 | CONP:Canadian Open Neuroscience Platform | 2026-08-21 12:41:04 | 11 | ||||||
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FFTW Resource Report Resource Website 10+ mentions |
FFTW (RRID:SCR_016554) | FFTW | software library, software resource, software toolkit | Software as a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). | library, collection, fast, C routine, compute, discrete, Fourier, transform | has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; | DOI:10.1109/JPROC.2004.840301 | Free, Available for download, Freely available | SCR_016554 | Fastest Fourier Transform in the West | 2026-08-21 12:40:52 | 17 | |||||||
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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 | 2026-08-21 12:40:49 | 518 | ||||||||||
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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 | 2026-08-21 12:40:56 | 0 | |||||||
|
Frozen Noise Resource Report Resource Website 1+ mentions |
Frozen Noise (RRID:SCR_016558) | data analysis software, data processing software, software application, software resource, software toolkit | Software analysis tools for electrophysiological somatosensory cortex databank. Allows to estimate the information content of spiking in single neuron resolution. It accompanies the open source intracellular recording database by Lantyer and colleagues. | electrophysiological, somatosensory, cortex, estimate, spiking, single, neuron, resolution | is related to: MATLAB | Free, Available for download, Freely available | SCR_016558 | 2026-08-21 12:40:52 | 4 | ||||||||||
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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 | 2026-08-21 12:40:54 | 84 | ||||||||||
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User Friendly Functional Connectivity - UF²C Resource Report Resource Website 1+ mentions |
User Friendly Functional Connectivity - UF²C (RRID:SCR_016550) | UF²C | data analysis software, data processing software, image analysis software, software application, software resource, software toolkit | Software tool to standardize and facilitate connectivity studies through a graphical user interface and validated preset parameters. | standardize, functional, connectivity, brain, magnetic, resonance, imaging, graphical, user, interface, parameter |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: MATLAB |
FAPESP | Free, Available for download, Freely available | SCR_016550 | User Friendly Functional Connectivity | 2026-08-21 12:40:52 | 1 | |||||||
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Sleep Heart Health Study Resource Report Resource Website 50+ mentions |
Sleep Heart Health Study (RRID:SCR_016559) | SHHS | data or information resource, disease-related portal, portal, topical portal | Portal for a multi-cohort study focused on sleep-disordered breathing and cardiovascular outcomes implemented by the National Heart Lung and Blood Institute. Recorded signals are: EEG, ECG, EOG, SaO2, HR, EOG, EMG, respiratory inductance plethysmography, respiration (thermistor), position, light. | dataset, analysis, sleep, apnea, breathing, disorder, cardiovascular, disease, EEG, ECG, respiration, PSG | is listed by: National Sleep Research Resource (NSRR) | sleep disorder, sleep apnea, cardiovascular disease | NHLBI U01 HL53916; NHLBI U01 HL53931; NHLBI U01 HL53934; NHLBI U01 HL53937; NHLBI U01 HL53938; NHLBI U01 HL53941; NHLBI U01 HL64360 |
PMID:9493915 | Free, Freely available, Registration required for membership | SCR_016559 | Sleep Heart Health Study | 2026-08-21 12:41:06 | 84 | |||||
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Praat Resource Report Resource Website 100+ mentions |
Praat (RRID:SCR_016564) | data analysis software, data processing software, software application, software resource | Software tool for phonetics research to analyse, synthesize, and manipulate speech. | phonetics, analyse, systhetize, speech | Free, Available for download, Freely available, Tutorial available | http://www.praat.org, https://github.com/praat/praat/blob/master/fon/manual_tutorials.cpp | SCR_016564 | 2026-08-21 12:41:06 | 123 | ||||||||||
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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 | 2026-08-21 12:40:56 | 5 | ||||||
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Stitching Resource Report Resource Website 1+ mentions |
Stitching (RRID:SCR_016568) | data processing software, image analysis software, image processing software, image reconstruction software, software application, software resource | Software package available through Fiji to image large biological specimen at high resolution. Comes with 2 different plugins to reconstruct big images/stacks : Pairwise Stitching to stitch two 2d-5d images, and Grid/Collection Stitching to stitch an arbitrary amount of 2d-5d input images. | biological, speciment, resoultion, reconstruct, big, image, stack, stitching | Free, Available for download, Freely available | https://github.com/fiji/Stitching/releases/tag/Stitching_-3.1.3 | SCR_016568 | 2026-08-21 12:40:52 | 4 | ||||||||||
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Docker Desktop Resource Report Resource Website 10+ mentions |
Docker Desktop (RRID:SCR_016445) | DD | software application, software development environment, software development tool, software resource | Software development environment that helps users build containerized software using Docker and Kubernetes softwares. It is executable on desktop and cloud, and allows access to a vast library of community containerized content in Docker Hub. | software, container, build, code, coding, containerize, develop, development, environment, application | Free, Commercially available, Requires account to download, Available for download | SCR_016445 | Docker, DockerDesktop | 2026-08-21 12:41:05 | 26 | |||||||||
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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 | 2026-08-21 12:40:56 | 160 | ||||
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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 | 2026-08-21 12:41:05 | 186 | ||||||
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MCTrace Resource Report Resource Website 1+ mentions |
MCTrace (RRID:SCR_016532) | data analysis software, data processing software, image analysis software, software application, software resource | Software tool as a program for building skeletonized models of 3D structures with a graphical user interface. GUI based neuronal network model building. | build, skeletonized, model, 3D structure, neuronal, network | Free, Available for download, Freely available | SCR_016532 | 2026-08-21 12:40:56 | 3 | |||||||||||
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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 | 2026-08-21 12:41:05 | 548 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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