Curator Dashboard

Developed for Allen Reference Atlas and follows terminology from Brain Maps: Structure for the Rat Brain (Swanson, 2004, 2018). The ontology has been subsequently extended and revised to also serve as structure ontology for Allen Mouse Common Coordinate Framework.Defines hierarchical partonomy of anatomical structures of adult mouse brain. At top level, brain is divided into gray matter, fiber tracts and ventricular systems. Gray matter is subdivided into cerebrum, brain stem, and cerebellum, which are themselves organized into subregions in hierarchical tree.

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• RRID-Legacy
• 5 years ago - submitted by Lydia Ng

3D reference atlas to use with online datasets or as standalone resources. Can be used to analyze, visualize, and integrate multimodal and multiscale datasets in 3D. Intensity and shape population average template brain serves as basis of reference space and coordinate system. Average was constructed at 10 um voxel resolution by interpolating high resolution serial two photon tomography images from young adult C57BL/6J mice. Using multimodal reference data, entire brain was directly parcellated in 3D, labeling every voxel with brain structure from Allen Mouse Reference Atlas Ontology. In the 2017 release, the parcellation spanned 43 isocortical areas and their layers, 329 subcortical gray matter structures, 81 fiber tracts, and 8 ventricular structures.

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• RRID-Legacy
• 5 years ago - submitted by Lydia Ng

Nonprofit facility providing researchers worldwide with standardized, high-quality primary airway cells from normal and large variety of airway diseased donors with different genetic backgrounds, are essential for improving our understanding of CF and other respiratory diseases and for translational research to develop new therapeutic agents.The PACB is certified by the UBC Office of Biobank Education and Research Biobank Certification Program.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Center composes network of core imaging facility locations for advanced optical imaging and basic electron microscopy located within the AHC/Medical School (1-151 Jackson Hall, Minneapolis) and College of Biological Sciences (23 Snyder Hall, St. Paul) on the University of Minnesota Twin Cities Campus.UIC cores serve internal and external research clients in design of imaging experiments, choice of and training on suitable imaging systems, and subsequent image processing, visualization and analysis.Provides advanced imaging systems including macro spectral confocal microscopy,wide-field light and fluorescence microscopy, spinning disk confocal, laser-scanning confocal microscopes, multi photon/Second Harmonic Generation microscopes, total internal reflectance microscope, laser capture micro-dissection, live cell imaging systems, scanning and transmission electron microscopy, whole animal fluorescence, bioluminescence and chemiluminescence imagers, gel, print and film scanners,poster printers, full sample preparation capabilities.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core offers instrumentation and services for study of biological processes at whole animal, tissue, cellular and subcellular levels. This includes light microscopy, electron microscopy and image analysis. Light microscopy offerings include super resolution microscopy (MINFLUX, STED, NSPARC, SORA), fluorescent laser scanning and spinning disk microscopy, fluorescent lifetime imaging, automated high throughput tissue cytometry, atomic force microscopy, laser capture microdissection, mutliphoton imaging, and whole animal bioluminescent and fluorescent imaging. Electron microscopy includes sample prep and imaging for TEM, SEM, platinum replicas, immuno gold and CLEM. We also provide microinjection equipment, chambers for stable live cell observation, and anesthesia equipment. CAM provides training on numerous different instrument platforms, consultation on experiment design, as well as digital image processing and image analysis.CAM is one of two Nikon Imaging Centers in the US, allowing us access and excellent support from Nikon to develop innovative solutions for the cutting edge imaging needs of users.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software tool to allow characterization of parameters analyzed in fundamental and clinical studies in skeletal muscle field. Running on open source Fiji software platform, simultaneously analyzes parameters from immunofluorescent staining, imaged by different acquisition systems in completely automated manner.Used to analyze muscle cross-sectional area, fiber typing, localization of nuclei within muscle fiber, number of vessels, fiber associated stem cells parameters simultaneously.

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• RRID-Legacy
• 5 years ago - by Anonymous

Open access software platform to faciliate calculation of quantities related to light and lighting. Users can upload spectra and platform will calculate relevant quantites including luminance, chromaticity, and α-opic radiance and α-opic daylight luminances from spectra, generate visualisation of spectrum, and enable export of calculations in tabular form.

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• RRID-Legacy
• 5 years ago - submitted by Manuel Spitschan

Software tool for pathology slide viewing. Used for access to color digital slide images to which you can adjust magnification, pan and zoom, compare different stains, annotate areas of interest, perform image analysis, and more. Allows to view slide images taken by Leica biosystems scanner.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool as Javascript encoder and decoder to use spectral power distributions in URL.

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• RRID-Legacy
• 5 years ago - submitted by Michael Herf

Cloud based research platform that allows researchers and students to quickly and easily create and deploy behavioural experiments online. Online behavioral experiment builder for running behavioural studies.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling.

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• RRID-Legacy
• 5 years ago - by Anonymous

The Gruss Lipper Precision Instrumentation Technologies (PIT) Resource Center provides access to various fabrication and rapid prototyping tools for qualified users. The PIT allows users to design and build their own research tools by providing access to wide array of prototyping and fabrication equipment, as well as design and fabrication consultation. The PIT also provides full prototyping service (design through fabrication and testing).

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Rockefeller University Spectroscopy Resource Center Core Facility RESOURCE IS NO LONGER IN SERVICE, documented on February 14, 2022. The core was merged with Rockefeller University Fisher Drug Discovery Resource Center Core Facility. Core provides spectroscopic and calorimetric equipment for use in studies of structure, function and interactions of biological and organic molecules.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core offers mass spectrometry services and associated technologies to the University of Manchester and beyond with focus on biological molecules such as proteins and metabolites in proteomics and metabolomics areas.Provides support from experimental design to advanced sample preparation and data processing and interpretation.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core offers services and instruments to support genomics research. Houses Illumina NovaSeq, NextSeq, MiSeq sequencers, 10X Genomics Chromium Single Cell System, and Life Technologies QuantStudio 12K flex realtime PCR system. Provides several accessory instruments for sample quantity and quality validation: Agilent Bioanalyzer, Agilent TapeStation, NanoDrop spectrophotometer, and Qubit spectrophotometer.Offers full services for genomic DNA-Seq and RNA-Seq, specializing in preparation of libraries from very small amount of starting total RNA. Users can also prepare their own libraries and use the center�s sequencing-only services. Offers free consultations on experimental designs, library preparation options, sequencer choice, sequencing depth and coverage, and biological replicates.Performs initial sequencing data analysis for all users, and can assist with downstream analysis.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Core guides researchers in drug discovery by improving efficiency of their bioassays, identifying compounds and targets of function, and in utilizing technologies for measurement of drug/receptor interactions.Center also has spectroscopic and calorimetric equipment for use in studies of interactions of drugs with their targets.

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• SciCrunch
• 5 years ago - submitted by Edyta Vieth

Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software toolbox, formerly called CPMjs, as framework to build interactive, explorable simulation models of cells and tissues in web browser. JavaScript library to build interactive Cellular Potts Models as command line applications or in web browser.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

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• dkNET
• 5 years ago - submitted by Ko-Wei Lin

Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.

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• dkNET
• 5 years ago - submitted by Ko-Wei Lin