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https://www.nitrc.org/projects/qcalign
Software tool to detect regions that are affected by tissue damage, labelling defects, artifacts or errors in image acquisition, regions that are poorly registered, or where registration cannot be verified. Makes it easier for the user to explore the atlas hierarchy and decide on customized hierarchy level for investigation. QCAlign was developed to support QUINT workflow which supports spatial analysis of labelling in series of brain sections from mouse and rat based on registration to reference atlas.
Proper citation: QCAlign (RRID:SCR_023088) Copy
Joint computational research center with Carnegie Mellon University and University of Pittsburgh. Provides university, government and industrial researchers with access to several systems for high performance computing, communications and data storage available to scientists and engineers nationwide for unclassified research.
Proper citation: Pittsburgh Supercomputing Center (RRID:SCR_022823) Copy
https://github.com/vesselman/SparkAn
Software tool for custom calcium imaging analysis.
Proper citation: SparkAn (RRID:SCR_022028) Copy
https://rewireneuro.com/product/pipsqueak/
Software image analysis tool as older ImageJ/Fiji plugin version.
Proper citation: Pipsqueak AI (RRID:SCR_022149) Copy
https://opencell.czbiohub.org/
Proteome scale collection of protein localization and interaction measurements in human cells. Proteome scale endogenous tagging enables cartography of human cellular organization.
Proper citation: OpenCell (RRID:SCR_021870) Copy
https://isamplesorg.github.io/home/
Project to align physical sample identifiers. Used to design, develop, and promote service infrastructure to uniquely, consistently, and conveniently identify material samples, record metadata about them, and persistently link them to other samples and derived digital content, including images, data, and publications.
Proper citation: iSamples (RRID:SCR_021750) Copy
Collection as result of joint work of scientists, technicians and students from Federal University of Rio de Janeiro and Technical-Scientific Association Paul Ehrlich. Center of reference and excellence in cell culture in Brazil and in our continent. Collection of human and animal cells that operates as service provider in Brazil and is the largest in South America.
Proper citation: Rio de Janeiro Cell Bank (RRID:SCR_023181) Copy
https://catalog.bcrc.firdi.org.tw/
Systematic and service oriented BioResource Center in Asia. Member of World Federation for Culture Collections from 1984 until now. BCRC is the first BRC certified by international organization of ISO quality system. Approved by Taiwan Biodiversity Information Facility.
Proper citation: Taiwan Bioresource Collection and Research Center (RRID:SCR_023180) Copy
https://finngen.gitbook.io/documentation/
Public private partnership combining genotype data from Finnish biobanks and digital health record data from Finnish health registries. Provides opportunity to study genetic variation in relation to disease trajectories in isolated population.
Proper citation: FinnGen (RRID:SCR_022254) Copy
https://cellbank.nibiohn.go.jp/english/
Collection of various human and animal culture cells including cancer and genetically modified cells. Cell resources are distributed to researchers across Japan and around the world. These cells are comprehensively qualified by testing microbial contamination, virus contamination and cross culture contamination. Some cells are characterized by karyotyping and/or cell surface markers. In collaboration with other major cell banks in the world, we are developing methods for cell culturing and quality control in order to support fundamental research on medical of pharmaceutical sciences.
Proper citation: Japanese Collection of Research Bioresources Cell Bank (RRID:SCR_023187) Copy
Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution.
Proper citation: BCALM 2 (RRID:SCR_023975) Copy
Collection of foundational software libraries, upon which ImageJ2 and Fiji are built. It is a collaboration of projects providing software for scientific computing in effort to cooperate and reuse code.
Proper citation: scijava (RRID:SCR_023335) Copy
Flagship initiative of Childrens Mercy Research Institute and Genomic Medicine Center in Kansas City. This research program is building pediatric data repository to facilitate search for answers and novel treatments.Goal is to collect genomic data and health information for 30,000 children and their families to create a database of genomes.
Proper citation: Genomic Answers for Kids (RRID:SCR_021840) Copy
https://www.syngene.com/software/genetools-automatic-image-analysis/
Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting.
Proper citation: GeneTools (RRID:SCR_022505) Copy
Center coordinates ideas and investments to advance and democratize access to Stanford cores, instrumentation, scientific and technical staff, allowing users to perform innovative, rigorous experiments.
Proper citation: Stanford University Community of Shared Advanced Research Platforms (RRID:SCR_022986) Copy
ROBOKOP system consists of web based user interface, API server, and several worker servers. Biomedical knowledge graph that integrates and semantically harmonizes important knowledge sources. Contains nodes representing entities such as genes, chemicals, and diseases, and edges representing relationships between them. Abstraction layer and user interface for knowledge graphs to support question answering. Used for reasoning over structured biomedical knowledge databases as part of NCATS translator and reasoner programs. ROBOKOP Knowledge Graph Builder constructs KG and provides extensible framework to handle graph query over and integration of federated data sources.
Proper citation: ROBOKOP (RRID:SCR_023437) Copy
https://freeimage.sourceforge.io/
Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications.
Proper citation: FreeImage (RRID:SCR_024022) Copy
GDCM includes file format definition and network communications protocol, both of which should be extended to provide full set of tools for researcher or small medical imaging vendor to interface with existing medical database.Implementation of DICOM standard designed to be open source so that researchers may access clinical data directly.
Proper citation: GDCM (RRID:SCR_024027) Copy
Project to promote and facilitate sharing of clinical trial data. Provides set of policies to set standards to enhance data availability and transparency in support of strong scientific research which aims to advance scientific and medical knowledge with goal of improving public health and healthcare delivery. Project has the final decision making rights regarding these policies and granting or denial of data requests, as per contractual agreements between the YODA Project and its partners.
Proper citation: Yoda Project (RRID:SCR_022761) Copy
Software tool to quantify comet parameters while studying DNA strand breaks. Automated tool for comet assay image analysis.
Proper citation: OpenComet (RRID:SCR_021826) Copy
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