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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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TrakEM2 Resource Report Resource Website 100+ mentions |
TrakEM2 (RRID:SCR_008954) | TrakEM2 | data processing software, software application, image analysis software, software resource | An ImageJ plugin for morphological data mining, three-dimensional modeling and image stitching, registration, editing and annotation. Two independent modalities exist: either XML-based projects, working directly with the file system, or database-based projects, working on top of a local or remote PostgreSQL database. What can you do with it? * Semantic segmentation editor: order segmentations in tree hierarchies, whose template is exportable for reuse in other, comparable projects. * Model, visualize and export 3D. * Work from your laptop on your huge, remote image storage. * Work with an endless number of images, limited only by the hard drive capacity. Dozens of formats supported thanks to LOCI Bioformats and ImageJ. * Import stacks and even entire grids (montages) of images, automatically stitch them together and homogenize their histograms for best montaging quality. * Add layers conveniently. A layer represents, for example, one 50 nm section (for TEM) or a confocal section. Each layer has its own Z coordinate and thickness, and contains images, labels, areas, nodes of 3d skeletons, profiles... * Insert layer sets into layers: so your electron microscopy serial sections can live inside your optical microscopy sections. * Run any ImageJ plugin on any image. * Measure everything: areas, volumes, pixel intensities, etc. using both built-in data structures and segmentation types, and standard ImageJ ROIs. And with double dissectors! * Visualize RGB color channels changing the opacity of each on the fly, non-destructively. * Annotate images non-destructively with floating text labels, which you can rotate/scale on the fly and display in any color. * Montage/register/stitch/blend images manually with transparencies, semiautomatically, or fully automatically within and across sections, with translation, rigid, similarity and affine models with automatically extracted SIFT features. * Correct the lens distortion present in the images, like those generated in transmission electron microscopy. * Add alpha masks to images using ROIs, for example to split images in two or more parts, or to remove the borders of an image or collection of images. * Model neuronal arbors with 3D skeletons (with areas or radiuses), and synapses with connectors. * Undo all steps. And much more... | java, imagej plugin, neuronal circuit, reconstruction, electron microscopy, optical image volume, arbor, synapse, image, align, register, FASEB list |
is listed by: 3DVC is related to: Segmented ssTEM stack of neural tissue is related to: ImageJ has parent organization: University of Zurich; Zurich; Switzerland |
Swiss National Science Foundation 31003A_132969; NINDS 1-R01 NS054814-05 |
PMID:22723842 PMID:20957184 |
If your work uses TrakEM2 or its associated image registration libraries, Please cite. | nlx_151924 | SCR_008954 | 2026-08-15 11:28:05 | 344 | ||||||
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University of Zurich; Zurich; Switzerland Resource Report Resource Website 1+ mentions |
University of Zurich; Zurich; Switzerland (RRID:SCR_000342) | UZH | university | University located in Zürich, Switzerland was founded in 1833. Has faculties in Philosophy, Human Medicine, Economic Sciences, Law, Mathematics and Natural Sciences, Theology and Veterinary Medicine. Offers the widest range of subjects and courses of any Swiss higher education institution. As of October 2018, 23 Nobel laureates and 1 Turing Award winner have been affiliated with University of Zurich as alumni, faculty or researchers. | immunology, genetics, neuroscience, structural biology, medicine, master, bachelor, phd |
is parent organization of: Connectome Wiki is parent organization of: Swiss Institute of Allergy and Asthma Research is parent organization of: MLTreeMap is parent organization of: University of Zurich SCRM - Cell-and Tissue Biobank is parent organization of: HPC-CLUST is parent organization of: Segmented ssTEM stack of neural tissue is parent organization of: Low Resolution Electromagnetic Tomography is parent organization of: Institute of Neuroinformatics is parent organization of: Institute for Neuroinformatics: Cortex 3D is parent organization of: TrakEM2 is parent organization of: B-Fabric is parent organization of: MINAS - Metal Ions in Nucleic AcidS is parent organization of: sLORETA is parent organization of: exact Low Resolution Electromagnetic Tomography is parent organization of: Grid Enabled Molecular Science Through Online Networked Environments is parent organization of: CATALYSTLite is parent organization of: imctools is parent organization of: Hierarchical Unsupervised Generative Embedding toolbox is parent organization of: PAXdb is parent organization of: University of Zurich Center for Microscopy and Image Analysis Core Facility is parent organization of: Progenetix |
nlx_15354 | SCR_000342 | University of Zurich, Universitat Zurich | 2026-08-15 11:21:48 | 1 | ||||||||
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3DVC Resource Report Resource Website |
3DVC (RRID:SCR_001377) | 3DVC | community building portal, data or information resource, portal | THIS RESOURCE IS NO LONGER IN SERVICE, confirmed by curator 11/21/2018; Community of researchers attempting to build a comprehensive virtual cell model. The 3DVC will do for cell biology what the Large Hadron Collider (LHC) does for particle physics, but through a virtual rather than physical resource. It will bring together collaborators around a shared infrastructure to advance the field through efficient groundbreaking science and technology, the results of which will be broadly disseminated to an audience ranging from K12 to professionals. The 3DVC is committed to open science, yet strives for sustainability through new business models that leverages that open content. | cell, model, biological structure, molecule |
lists: Albinism database lists: ButterflyBase lists: G2P Knowledge Centre lists: Bio-Job.org lists: RettBASE: IRSF MECP2 Variation Database lists: Resource for Biocomputing Visualization and Informatics lists: National Center for Integrative Biomedical Informatics lists: Genome Network Platform lists: NeuroExplorer lists: Open Provenance Model lists: BarleyBase lists: BioModels lists: Arabidopsis Reactome lists: MEDLINE lists: bioDBcore lists: GermOnline lists: GlycoMapsDB lists: SNPHunter lists: Allen Institute for Brain Science Sleep Study lists: Coddle-Codons Optimized to Discover Deleterious LEsions lists: MicroArray and Gene Expression Markup Language lists: Fungal Genome Initiative lists: EMDataResource.org lists: University of Southern California LONI Software lists: Ontology Development and Information Extraction lists: Software Distribution Sets lists: L-Measure lists: UCSF Chimera lists: Zebrafish Neurophenome Project Database lists: Standards-based Infrastructure with Distributed Resources lists: HapMap 3 and ENCODE 3 lists: NCBI BioProject lists: SEQanswers Wiki lists: NIF Data Federation lists: SMD lists: SoyBase lists: modelcrop.org lists: BiGG Database lists: FSST - Functional Similarity Search Tool lists: LHP LHDL lists: Open Provenance Model Vocabulary lists: DiseaseMeth lists: neuroVIISAS lists: Predictive Networks lists: SitEx lists: NRCAM lists: DisGeNET lists: MCMBB lists: BARD lists: Mouse Genome Informatics (MGI) lists: European Nucleotide Archive (ENA) lists: Comparative Toxicogenomics Database (CTD) lists: PomBase lists: Stanford University HIV Drug Resistance Database lists: Database of Chemical Compounds and Reactions in Biological Pathways lists: UCSD-Nature Signaling Gateway Molecule Pages lists: IntAct lists: The WWW Virtual Library: Model Organisms lists: Helicobacter Pylori Database of Protein Interactomes lists: Genes to Cognition: Neuroscience Research Programme lists: neuroConstruct lists: ModelDB lists: 3DViewnix lists: TMRPres2D lists: Ikaros Project lists: Dockground: Benchmarks, Docoys, Templates, and other knowledge resources for DOCKING lists: Interagency Modeling and Analysis Group lists: Annozilla (Annotea on Mozilla) lists: Artificial Selected Proteins/Peptides Database lists: Cancer Chromosomes lists: CATMA - Complete Arabidopsis Transcriptome MicroArray lists: Combinatorial Extension (CE) lists: ChemDB: The UC Irvine ChemDB lists: CluSTr lists: CTDatabase lists: DRC - Database of Ribosomal Crosslinks lists: Gene Expression in Tooth Database lists: GenoBase lists: GPX-Macrophage lists: Hetero-compound Information Centre- Uppsala lists: IMG lists: InSatDb lists: InterDom lists: IPD-HPA - Human Platelet Antigens lists: Max Planck Unified Proteome Database lists: Molecular Modelling DataBase lists: MegaMotifbase lists: Metalloprotein Site Database lists: MitoDat - Mendelian Inheritance and the Mitochondrion lists: Madison Metabolomics Consortium Database lists: Olfactory Receptor DataBase lists: SUPERFAMILY lists: EyeBrowse lists: Allen Institute Mouse Diversity Study lists: BIRD - Bio Info R and D lists: Bioinformatics Links Directory lists: Electroencephalogram Database: Prediction of Epileptic Seizures lists: Human Protein-Protein Interaction Mining Tool lists: Interagency Modeling and Analysis Group and Multi-scale Modeling Consortium Wiki lists: Systems Biology Workbench lists: CellML lists: MathML lists: AraCyc lists: Biochemical Pathways database lists: CellML Model Repository lists: Cytokine Family Database lists: Bacterial Genomes lists: U.S. Pig Genome Project lists: ComBase: A Combined Database For Predictive Microbiology lists: GeneWindow lists: Comprehensive Systems-Biology Database lists: Candidate Genes to Inherited Diseases lists: MeGX lists: Mammalian Phosphorylation Resource lists: Efficient Mixed-Model Association lists: Proteome Analyst PA-GOSUB lists: PubCrawler lists: Conical: The Computational Neuroscience Class Library lists: Gene Expression Profile Analysis Suite lists: Adaptive Poisson-Boltzmann Solver lists: Aggrescan: The Hot Spot Finder lists: Distributed Annotation System lists: COILS: Prediction of Coiled Coil Regions in Proteins lists: DNAWorks at Helix Systems lists: Microarray DB lists: Gene Relationships Across Implicated Loci lists: SEQtools lists: DeRisi Lab lists: Protein Subcellular Location Image Database lists: Open Information Integration lists: Metagenomics Program at JGI lists: BrainPeps lists: EGAN: Exploratory Gene Association Networks lists: CBioC lists: OrChem lists: Generic GO Term Finder lists: G-node portal electrophysiology data sharing lists: LegumeIP lists: Roadmap Epigenomics Project lists: TrakEM2 lists: ATID: Alternative Translational Initiation Database lists: linked life data - a semantic data integration platform for the biomedical domain lists: Crux tandem mass spectrometry analysis software lists: CellProfiler Analyst lists: Scirus - for scientific information only lists: SRS lists: KEGG lists: Antibodypedia lists: SWISS-MODEL Repository lists: BTKbase lists: ExTopoDB lists: MINAS - Metal Ions in Nucleic AcidS lists: Tripod lists: NIH electronic Research Materials catalogue lists: Alliance for Cellular Signaling Molecule Pages Database lists: Death Domain database lists: Cube-DB lists: OntoQuest lists: EASE: the Expression Analysis Systematic Explorer lists: Greglist lists: Chloroplast Genome Database lists: Montage RTS2000 lists: BGI-RISe - Beijing Genomics Institute Rice Information System lists: ApiDB CryptoDB lists: Chilibot: Gene and Protein relationships from MEDLINE lists: AutDB lists: DAVID lists: Dataverse Network Project lists: Binding MOAD lists: Biological Magnetic Resonance Data Bank (BMRB) lists: RNAhybrid lists: RegulonDB lists: Artemis: Genome Browser and Annotation Tool lists: Genomedata lists: CATSS - Child and Adolescent Twin Study in Sweden lists: Viking Viewer for Connectomics lists: SpliceDB lists: Galaxy lists: SPM lists: Hyper Cell Line Database lists: MeGX has parent organization: University of California at San Diego; California; USA |
NSF 1216893 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_152536 | http://www.3dvcell.org/conference-toward-3d-virtual-cell | SCR_001377 | 3D Virtual Cell | 2026-08-15 11:22:05 | 0 | |||||
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Segmented ssTEM stack of neural tissue Resource Report Resource Website 1+ mentions |
Segmented ssTEM stack of neural tissue (RRID:SCR_007004) | Segmented ssTEM stack of neural tissue | image, data or information resource, data set | 30 sections from a serial section Transmission Electron Microscopy (ssTEM) data set of the Drosophila first instar larva ventral nerve cord (VNC). The microcube measures 2 x 2 x 1.5 microns approx., with a resolution of 4x4x50 nm/pixel. The images are representative of actual images in the real-world: there is a bit of noise; there are image registration errors; there is even a small stitching error in one section. None of these led to any difficulties in the manual labeling of each element in the image stack by an expert human neuroanatomist. A software application that aims at removing or reducing human operation must be able to cope with all these issues. Each labeled object has a unique id and fits into the overall datastructure of the data set. For example, each mitochondria is represented by a unique Arealist object, containing a list of labeled areas, one per section. All membranes have been highlighted as one unique object. All neurites (and glia) have been highlighted each as its own independent object, delimited by membrane and non-overlapping with membrane and with each other. On the other hand, mitochondria, noise and synapses overlap with membranes, neurites and glia; hence, they are offered as independent tif stacks. | ventral nerve cord, transmission electron microscopy, mitochondria, synapse, membrane, neurite, glia, noise, section |
is related to: TrakEM2 has parent organization: University of Zurich; Zurich; Switzerland |
PMID:20957184 | Free for the purpose of generating or testing non-commercial image segmentation software. If any scientific publications derive from the usage of this data set, You must cite as specified. | nlx_151926 | SCR_007004 | 2026-08-15 11:23:31 | 4 | |||||||
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ImageJ Resource Report Resource Website 10000+ mentions |
ImageJ (RRID:SCR_003070) | software toolkit, image analysis software, image processing software, data processing software, software application, software resource | Open source Java based image processing software program designed for scientific multidimensional images. ImageJ has been transformed to ImageJ2 application to improve data engine to be sufficient to analyze modern datasets. | image, data, processing, analysis, datasets, visualization, |
uses: NeuriteTracer is used by: Mouse Behavioral Analysis Toolbox is used by: Focinator is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: uManager is related to: Fiji is related to: NIH Image is related to: TrakEM2 is related to: BioVoxxel Toolbox is related to: Golddigger is related to: Analyze Complex Roots Tool is related to: Analyze Spheroid Cell Invasion In 3D Matrix is related to: PyImageJ has parent organization: Research Services Branch National Institutes of Mental Health has plug in: Diffusing Tensor Imaging in Java has plug in: OrientationJ has plug in: GRatio for ImageJ has plug in: BioVoxxel Toolbox has plug in: WormSizer has plug in: MultiStackReg has plug in: Iterative Deconvolve 3D has plug in: Thunder STORM has plug in: Whisker tracking macro has plug in: 3D Roi Manager has plug in: 3D Objects Counter has plug in: BoneJ has plug in: QuickFigures has plug in: ObjectJ has plug in: ADAPT has plug in: DHM Utilities has plug in: Sholl Analysis has plug in: nTracer has plug in: IHC Profiler has plug in: MicrobeJ has plug in: AccPbFRET has plug in: RiFRET has plug in: JaCoP has plug in: Cell Counter Plugin for ImageJ has plug in: Puncta Analyzer has plug in: SpinalJ has plug in: ColonyArea works with: Intensity Ratio Nuclei Cytoplasm Tool works with: 3D ImageJ Suite works with: Wound Healing Tool works with: MorphoLibJ |
NINDS ; NIGMS RC2 GM092519; Wellcome Trust Strategic Award 095931; the Laboratory for Optical and Computational Instrumentation ; the Morgridge Institute for Research ; NIH ; NIMH |
PMID:22930834 PMID:29187165 DOI:10.1038/nmeth.2089 |
Free, Available for download, Freely available | ascl:1206.013, rid_000070, Q1659584, 2012ascl.soft06013R, nif-0000-30467, SCR_018407 | https://imagej.net/ij/, http://rsbweb.nih.gov/ij, https://imagej.nih.gov/ij/download.html, https://imagej.nih.gov/ij/, https://sources.debian.org/src/imagej/, | https://imagej.nih.gov/ij/, http://www.nitrc.org/projects/incf_imagej, | SCR_003070 | Image J, ImageJ - Image Processing and Analysis in Java, ImageJ2, ImageJ | 2026-08-15 11:27:07 | 29025 |
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