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https://www.amnh.org/research/microscopy-and-imaging-facility

Shared instrumentation facility at the American Museum of Natural History with tools for X-ray tomography, electron microscopy, confocal microscopy, light microscopy and image analysis. Provides expert assistance in the use of all lab equipment.

Proper citation: American Museum of Natural History Microscopy and Imaging Core Facility (RRID:SCR_024760) Copy   

•   Source: SciCrunch Registry

https://sc.edu/study/colleges_schools/artsandsciences/centers_and_institutes/emc/index.php

Electron Microscopy Center at USC is core facility providing all levels of technical support and consultation in area of light microscopy, electron microscopy, and elemental analysis. Provides microscopy and specimen preparation services for biological and materials science research. Offers training and access to all microscopes and ancillary equipmen.

Proper citation: University of South Carolina Electron Microscopy Core Facility (RRID:SCR_026179) Copy   

•   Source: SciCrunch Registry

https://www.ifom.eu/en/cancer-research/technological-units/imaging.php

Core Facility provides technological platforms in the field of light microscopy. A team of highly qualified and experienced professionals supports IFOM's research activities, assisting in sample preparation and acquisition, data post-processing and image analysis.

Proper citation: Cancer Research Institute IFOM ALM Advanced Light Microscopy Core Facility (RRID:SCR_026866) Copy   

•   Source: SciCrunch Registry

http://ccdb.ucsd.edu/SAO

An ontology that describes structures from the dimensional range encompassing cellular and subcellular structure, supracellular domains, and macromolecules. It is built according to ontology development best practices (re-use of existing ontologies; formal definitions of terms; use of foundational ontologies). It describes the parts of neurons and glia and how these parts come together to define supracellular structures such as synapses and neuropil. Molecular specializations of each compartment and cell type are identified. The SAO was designed with the goal of providing a means to annotate cellular and subcellular data obtained from light and electron microscopy, including assigning macromolecules to their appropriate subcellular domains. The SAO thus provides a bridge between ontologies that describe molecular species and those concerned with more gross anatomical scales. Because it is intended to integrate into ontological efforts at these other scales, particular care was taken to construct the ontology in a way that supports such integration.

Proper citation: Subcellular Anatomy Ontology (RRID:SCR_003486) Copy   

•   Source: SciCrunch Registry

https://www.olympus-lifescience.com/en/microscopes/upright/bx53f2/

LED illuminator for BX53 is equivalent to or better than 100 W halogen lamp, delivering brightness appropriate for teaching or contrast methods. Can be customized for different observation methods, such as phase contrast and fluorescence, with modular components.

Proper citation: Olympus BX53 Upright Microscope (RRID:SCR_022568) Copy   

•   Source: SciCrunch Registry

http://ccdb.ucsd.edu

THIS RESOURCE IS NO LONGER IN SERVICE, documented June 5, 2017. It has been merged with Cell Image Library. Database for sharing and mining cellular and subcellular high resolution 2D, 3D and 4D data from light and electron microscopy, including correlated imaging that makes unique and valuable datasets available to the scientific community for visualization, reuse and reanalysis. Techniques range from wide field mosaics taken with multiphoton microscopy to 3D reconstructions of cellular ultrastructure using electron tomography. Contributions from the community are welcome. The CCDB was designed around the process of reconstruction from 2D micrographs, capturing key steps in the process from experiment to analysis. The CCDB refers to the set of images taken from microscope the as the Microscopy Product. The microscopy product refers to a set of related 2D images taken by light (epifluorescence, transmitted light, confocal or multiphoton) or electron microscopy (conventional or high voltage transmission electron microscopy). These image sets may comprise a tilt series, optical section series, through focus series, serial sections, mosaics, time series or a set of survey sections taken in a single microscopy session that are not related in any systematic way. A given set of data may be more than one product, for example, it is possible for a set of images to be both a mosaic and a tilt series. The Microscopy Product ID serves as the accession number for the CCDB. All microscopy products must belong to a project and be stored along with key specimen preparation details. Each project receives a unique Project ID that groups together related microscopy products. Many of the datasets come from published literature, but publication is not a prerequisite for inclusion in the CCDB. Any datasets that are of high quality and interest to the scientific community can be included in the CCDB.

Proper citation: Cell Centered Database (RRID:SCR_002168) Copy   

•   Source: SciCrunch Registry

http://www.wholebraincatalog.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 26, 2016. An open source, downloadable, 3d atlas of the mouse brain and its cellular constituents that allows multi-scale data to be visualized in a seamless way, similar to Google earth. Data within the Catalog is marked up with annotations and can link out to additional data sources via a semantic framework. This next generation open environment has been developed to connect members of the neuroscience community to facilitate solutions for today's intractable challenges in brain research through cooperation and crowd sourcing. The client-server platform provides rich 3-D views for researchers to zoom in, out, and around structures deep in a multi-scale spatial framework of the mouse brain. An open-source, 3-D graphics engine used in graphics-intensive computer gaming generates high-resolution visualizations that bring data to life through biological simulations and animations. Within the Catalog, researchers can view and contribute a wide range of data including: * 3D meshes of subcellular scenes or brain region territories * Large 2D image datasets from both electron and light level microscopy * NeuroML and Neurolucida neuronal reconstructions * Protein Database molecular structures Users of the Whole Brain Catalog can: * Fit data of any scale into the international standard atlas coordinate system for spatial brain mapping, the Waxholm Space. * View brain slices, neurons and their animation, neuropil reconstructions, and molecules in appropriate locations * View data up close and at a high resolution * View their own data in the Whole Brain Catalog environment * View data within a semantic environment supported by vocabularies from the Neuroscience Information Framework (NIF) at http://www.neuinfo.org. * Contribute code and connect personal tools to the environment * Make new connections with related research and researchers 5 Easy Ways to Explore: * Explore the datasets across multiple scales. * View data closely at high resolution. * Observe accurately simulated neurons. * Readily search for content. * Contribute your own research.

Proper citation: Whole Brain Catalog (RRID:SCR_007011) Copy   

•   Source: SciCrunch Registry

http://synapses.clm.utexas.edu

A portal into the 3D ultrastructure of the brain providing: Anatomy of astrocytes, axons, dendrites, hippocampus, organelles, synapses; procedures of 3D reconstruction and tissue preparation; as well as an atlas of ultrastructural neurocytology (by Josef Spacek), online aligned images, and reconstructed dendrites. Synapse Web hosts an ultrastructural atlas containing more than 500 electron micrographs (added to regularly) that identify unique ultrastructural and cellular components throughout the brain. Additionally, Synapse Web has raw images, reconstructions, and quantitative data along with tutorial instructions and numerous tools for investigating the functional structure of objects that have been serial thin sectioned for electron microscopy.

Proper citation: Synapse Web (RRID:SCR_003577) Copy   

•   Source: SciCrunch Registry

http://www.openmicroscopy.org/site/products/omero

Client-server software for management, visualization, and analysis of biological microscopy images. OMERO handles images in a secure central repository where users can view, organize, analyze and share data from anywhere with internet access. Work with images from a desktop app (Windows, Mac or Linux), from the web or from 3rd party software.

Proper citation: OMERO (RRID:SCR_002629) Copy   

•   Source: SciCrunch Registry

http://www.loni.usc.edu/Software/MBAT

A workflow environment bringing together heterogenous, online biological image resources, a user's image data and biological atlases in a concise, unified and intuitive workspace. The MBAT viewer displays multiple images on a single virtual canvas allowing easy side-by-side comparisons and image compositing. MBAT is written in Java so it is platform independent and is highly extensible through it's plugin architecture. MBAT integrates three distinct workspaces for online search, image alignment (registration) and image display: * Search Workspace: able to submit a query to multiple databases simultaneously and online literature searches. * Registration Workspace: performs 2D landmark based registration. * Viewer Workspace: displays & composites images and image volumes using high performance graphics hardware. * Atlas Viewer: allows navigation and interrogation of volumetric atlases. * Hierarchy Editor: create logical groupings of atlas labels.

Proper citation: Mouse BIRN Atlasing Toolkit (RRID:SCR_002814) Copy   

•   Source: SciCrunch Registry

http://catmaid.org/

A toolkit designed to navigate, share and collaboratively annotate massive image data sets of biological specimens. The interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. The interface is inspired by GoogleMaps, with which it shares basic navigation concepts, enhanced to allow the exploration of 3D biological image data acquired by optical or physical sectioning microscopy techniques. The interface enables seamless sharing of regions of interest through bookmarks and synchronized navigation through multiple registered data sets. With massive biological image data sets it is unrealistic to create a sustainable centralized repository. A unique feature of CATMAID is its partially decentralized architecture where the presented image data can reside on any Internet accessible server and yet can be easily cross-referenced in the central database. In this way no image data are duplicated and the data producers retain full control over their images. CATMAID is intended to serve as data sharing platform for biologists using high-resolution imaging techniques to probe large specimens. Any high-throughput, high-content imaging project such as gene expression pattern screens would benefit from the interface for data sharing and annotation. Features: * Fast terabyte-scale image data browsing * Collaborative microcircuit reconstruction and annotation * Flexible hierarchical semantic annotation * Multiple linked image stack display * Neuron Catalog * SVG and WebGL-based neuronal morphology viewer * Open source software

Proper citation: CATMAID (RRID:SCR_006278) Copy   

•   Source: SciCrunch Registry

http://ncmir.ucsd.edu/

Biomedical technology research center that develops computer-aided, advanced microscopy for the acquisition of structural and functional data in the dimensional range of 1 nm to 100 um, a range encompassing macromolecules, subcellular structures and cells. Novel specimen-staining methods, imaging instrumentsincluding intermediate high-voltage transmission electron microscopes (IVEMs) and high-speed, large-format laser-scanning light microscopesand computational capabilities are available for addressing mesoscale biological microscopy of proteins and macromolecular complexes in their cellular and tissue environments. These technologies are developed to bridge understanding of biological systems between the gross anatomical and molecular scales and to make these technologies broadly available to biomedical researchers. NCMIR provides expertise, infrastructure, technological development, and an environment in which new information about the 3D ultrastructure of tissues, cells, and macromolecular complexes may be accurately and easily obtained and analyzed. NCMIR fulfills its mission through technology development, collaboration, service, training, and dissemination. It aims to develop preparative methods and analytical approaches to 3D microscopy applicable to neurobiology and cell biology, incorporating equipment and implementing software that expand the analysis of 3D structure. The core research activities in the areas of specimen development, instrument development, and software infrastructures maximize the advantages of higher voltage electron microscopy and correlated light microscopies to make ambitious imaging studies across scales routine, and to facilitate the use of resources by biomedical researchers. NCMIR actively recruits outside users who will not only make use of these resources, but who also will drive technology development and receive training.

Proper citation: National Center for Microscopy and Imaging Research (RRID:SCR_002655) Copy   

•   Source: SciCrunch Registry

http://www.incf.org/about/who-we-are/nodes/switzerland

Portal to promote the activities of Swiss research groups working in the field of neuroinformatics, and encourage and facilitate collaborations both between them and with the wider International Neuroinformatics Coordinating Facility community. The initial focus is on neural reconstruction as a theme, both from image data acquired via light microscopy and electron microscopy; these data are invaluable for identifying neural circuits and the simulation and modelling of these systems. Open Source software packages developed for neuroinformatics in Switzerland and useful data sets provided by groups in Switzerland are freely available for use, subject to appropriate attribution.

Proper citation: INCF Swiss Node (RRID:SCR_006284) Copy   

•   Source: SciCrunch Registry

https://le.ac.uk/cbs/facilities/aif

Open access light microscopy facility of College of Life Sciences. Offers wide range of confocal and conventional fluorescence microscopes and image analysis resources. AIF is part of Core Biotechnology Services CBS.

Proper citation: University of Leicester Advanced Imaging Facility (RRID:SCR_020967) Copy   

•   Source: SciCrunch Registry

https://nif.hms.harvard.edu/

Open access light microscopy and tissue core located within Neurobiology Department. Provides services in optical imaging, tissue clearing, in situ hybridization as well as introduces new equipment and cutting technology to the basic science community. Provides expertise, equipment, services and learning opportunities to researchers in the greater Boston area.

Proper citation: Harvard Medical School Neurobiology Imaging Core Facility (RRID:SCR_009808) Copy   

•   Source: SciCrunch Registry

https://www.ohsu.edu/advanced-light-microscopy-core

Provides confocal image analysis and presentation training, microscope training, microscope access service, deconvolution training, super resolution imaging and training service. Offers research scientists access to high-end instrumentation for fluorescence microscopy. Offers support with image acquisition, processing, analysis and presentation.

Proper citation: OHSU Advanced Light Microscopy Core Facility (RRID:SCR_009961) Copy   

•   Source: SciCrunch Registry

http://meharry.eagle-i.net/i/00000135-2fc1-b5b8-9658-54ab80000000

Core facility that provides the following services: Confocal and wide-field microscopy services, Confocal and wide-field microscopy training. It is the mission of the Meharry Medical College Morphology Core to provide the expertise and state-of-the-art instrumentation necessary to facilitate and enhance the productivity of Meharry?s investigators and trainees in the areas of fluorescence and bright-field microscopy and immunohistochemistry. This core strives to accomplish this by offering consultation on instrumentation and experimental design, training on instrumentation, and collaboration opportunities. We do our utmost to stay on the cutting edge of technology, skills, and knowledge in the field.

Proper citation: Meharry Morphology Core (RRID:SCR_009954) Copy   

•   Source: SciCrunch Registry

https://research.bidmc.org/confocal-imaging-core

Core facility that provides immunostaining (frozen and paraffin embedded tissues) and image processing services in confocal microscopy, light microscopy and immunostaining for cells and tissues including confocal microscopy, brightfield and fluorescence microscopy, and immunoperoxidase and immunofluorescence staining. BIDMC Immunostaining and Microscopy Core offers consultation and service for tissue immunostaining with paraffin or frozen sections, and for training to use confocal and widefield microscopes.

Proper citation: Beth Israel Deaconess Medical Center Confocal Imaging Core Facility (RRID:SCR_012312) Copy   

•   Source: SciCrunch Registry

https://med.virginia.edu/advanced-microscopy-facility/

Advanced Microscopy Facility is microscopy service and shared instrumentation facility in University of Virginia biomedical research community. Pprovides expertise and instrument access for electron and light microscopy imaging technologies as well as image analysis tools and services for basic scientists and clinical researchers within University of Virginia and across Commonwealth.

Proper citation: Virginia University School of Medicine Advanced Microscopy Core Facility (RRID:SCR_018736) Copy   

•   Source: SciCrunch Registry

https://www.research.uky.edu/pathology-core

Core facilitates COCVD projects by providing equipment and technical expertise to paraffin-embed and section tissue specimens and perform chemical staining of tissue sections to be examined, photographed and analyzed chromogenically by light microscopy.Training in immunohistochemical staining is available.

Proper citation: University of Kentucky College of Medicine, Lexington, Pathology Research Core Facility (RRID:SCR_018824) Copy   

•   Source: SciCrunch Registry