Curator Dashboard

Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

System to extend constant distance mode mass spectrometry imaging using nanospray desorption electrospray ionization by integrating shear force probe with nano DESI probe to improve imaging capabilities. Used for imaging biological samples of complex topography in their native states. Enables ambient imaging of biological samples with high sensitivity and minimal sample pretreatment.

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• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes.

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• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

Software tool as supervised machine learning algorithm that classifies and sorts single cell mass cytometry data according to their cell cycle, which allows to correct for cell cycle state and cell volume heterogeneity. Reveals signaling relationships and cell heterogeneity that were otherwise masked. Computational method to quantify cell cycle and cell volume variability.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

Software R package to provide pipeline for preprocessing of cytometry data, including normalization using bead standards, single cell deconvolution, and bead based compensation.

• Resource
• SciCrunch
• 8 years ago - submitted by Edyta Vieth

Software tool as interactive Shiny web application that provides user interface to mass cytometry data processing pipeline implemented in CATALYST R Bioconductor package.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

Software system for storing and analyzing high throughput B and T cell immune receptor sequencing data. Comprised of web interface and of Python analysis tools to process raw reads for gene usage, infer clones, aggregate data, and run downstream analyses, or in conjunction with other AIRR tools using its import and export features.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Anh Nguyet Vu

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

• Resource
• NIF
• 8 years ago - by Anonymous

Web service as calculator for statistics and analysis. Used on variety of browsers as well as mobile and tablet devices.They include Z-score, sample size, t value, One Way ANOVA Calculator, Percentile Calculator, Chi Square, p Value, and more.

• Resource
• SciCrunch
• 8 years ago - by Anonymous

Software tool for orthology analysis to identify orthologs, paralogs and co orthologs for genomes. Used to perform homology classification across genomes of different species in large genomic datasets.

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• SciCrunch
• 8 years ago - submitted by xiao hu

Software tool as graph based unsupervised biclustering algorithm to identify alterations in tumors based on hypothesis that gene pairs relevant to clinical process share statistically significant number of samples with extreme expression.

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• RRID-Legacy
• 8 years ago - submitted by Hossein Khiabanian

Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Michael Jochum

Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.

• Resource
• RRID-Legacy
• 8 years ago - by Anonymous

Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.

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• SciCrunch
• 8 years ago - submitted by Julien Bane

InterProScan 5: genome-scale protein function classification

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• SciCrunch
• 8 years ago - submitted by Julien Bane

A antibody for Servicebio

• Resource
• SciCrunch
• 8 years ago - submitted by shanshan liu

A data platform is designed to ingest, harmonize, aggregate, store, visualize, and disseminate human invasive neurophysiology data from BRAIN Initiative investigations. It provides a seamless interface for researchers uploading data and novel, intuitive ways for users to search and analyze the archive’s contents. In addition to comprehensive search, download, and data upload functionality, as well as streamlined data upload capabilities, DABI includes an interactive data visualization environment and integration with a suite of data-processing tools. DABI accommodates a wide variety of invasive neurophysiology data types, as well as imaging, behavioral and clinical data, in order to create a comprehensive picture of the human brain in health and disease. The infrastructure supporting DABI is comprised of fail-safe, redundant and secure components, more than 7PB of storage capacity and significant compute power.

• Resource
• RRID-Legacy
• 8 years ago - submitted by Anita Bandrowski

Organize, Store, Disseminate, Analyze and Visualize Invasive Neurophysiology Data. Shared archive and resource for human invasive neurophysiology data that have been established by Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative along with software tools for data uploading, visualization and analysis. Users can view and query datasets through online interface but cannot access raw data. Platform utilizes centralized and federated model. Investigators may upload data to central archive or house it themselves.

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• RRID-Legacy
• 8 years ago - submitted by Anita Bandrowski

Web application for Quantitative Trait Loci mapping via bulk segregant analysis of yeast sequencing data. Application provides automated data processing, annotations, and web interface to explore identified QTLs.

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• SciCrunch
• 8 years ago - submitted by Zhi Zhang