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http://www.moleculardevices.com/systems/metamorph-research-imaging/metafluor-fluorescence-ratio-imaging-software

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software designed to take single or multi-wavelength intracellular ion measurements an provide simultaneous display of the raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image for microscope techniques such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities.

Proper citation: MetaFluor Fluorescence Ratio Imaging Software (RRID:SCR_014331) Copy   

•   Source: SciCrunch Registry

https://github.com/lucadellasantina/ObjectFinder

Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes.

Proper citation: ObjectFinder (RRID:SCR_023319) Copy   

•   Source: SciCrunch Registry

https://neuromorpho.org/xyz2swc/ui/

Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface.

Proper citation: xyz2swc (RRID:SCR_023317) Copy   

•   Source: SciCrunch Registry

https://github.com/PedroBarbosa/VETA

Software tool that analyses performance of several variant prediction methods at different levels. Used to benchmark variant effect predictors from VCF files.

Proper citation: Variant Prediction Tools Evaluation (RRID:SCR_023314) Copy   

•   Source: SciCrunch Registry

https://precisionhealth.umich.edu/our-research/michigangenomics/

Collaborative research effort among physicians, researchers, and patients at the University of Michigan with goal of combining patient electronic health record data with corresponding genetic data to gain novel biomedical insights. Biobank linking genotypes and electronic clinical records in Michigan Medicine patients. MGI participants agree to provide study team with access to EHR data for clinical information and biospecimen including blood or saliva.

Proper citation: Michigan Genomics Initiative (RRID:SCR_023556) Copy   

•   Source: SciCrunch Registry

https://github.com/frlender/DendroX

Web application for multi-level multi-cluster selections in dendrogram. Provides interactive visualization of dendrogram in which users can divide dendrogram at any level and into any number of clusters.

Proper citation: DendroX (RRID:SCR_023434) Copy   

•   Source: SciCrunch Registry

https://cells.ucsc.edu/

Web based tool to visualize gene expression and metadata annotation distribution throughout single cell dataset or multiple datasets. Interactive viewer for single cell expression. You can click on and hover over cells to get meta information, search for genes to color on and click clusters to show cluster specific marker genes.

Proper citation: UCSC Cell Browser (RRID:SCR_023293) Copy   

•   Source: SciCrunch Registry

https://mskkp.org/

Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data.

Proper citation: Musculoskeletal Knowledge Portal (RRID:SCR_023171) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/roifile/

Software Python package to read, write, create, and plot ImageJ ROI format, an undocumented and ImageJ application specific format to store regions of interest, geometric shapes, paths, text, and whatnot for image overlays.

Proper citation: roifile (RRID:SCR_023331) Copy   

•   Source: SciCrunch Registry

http://cell-innovation.nig.ac.jp/maser/AllPipelines/P000001138_en.html

Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.

Proper citation: loadBAM2ge_db (RRID:SCR_015951) Copy   

•   Source: SciCrunch Registry

https://www.perkinelmer.com/product/harmony-5-1-office-hh17000012

Software tool designed by PerkinElmer for high content screening systems. Used to quantify complex cellular phenotypes. High content analysis software.

Proper citation: Harmony (RRID:SCR_023543) Copy   

•   Source: SciCrunch Registry

https://www.enroll-hd.org

Clinical research platform and longitudinal observational study for Huntington’s Disease families intended to accelerate progress towards therapeutics. Collaboration between Huntington’s disease families, clinicians, and researchers to accelerate progress toward effective treatments.

Proper citation: Enroll-HD (RRID:SCR_023300) Copy   

•   Source: SciCrunch Registry

https://github.com/pirovc/grimer

Software tool to perform analysis of microbiome studies and generates portable and interactive dashboard integrating annotation, taxonomy and metadata with focus on contamination detection.

Proper citation: GRIMER (RRID:SCR_023265) Copy   

•   Source: SciCrunch Registry

https://www.gehealthcare.com/products/advanced-visualization/all-applications/volume-viewer

Software tool to provide data 3D visualization and processing. Used for reading and comparing CT, MR, 3D X-ray, PET, and PET/CT datasets.

Proper citation: GE Volume Viewer (RRID:SCR_023417) Copy   

•   Source: SciCrunch Registry

https://github.com/vpc-ccg/svict

Software tool for detecting structural variations from cell free DNA containing low dilutions of circulating tumor DNA.

Proper citation: SViCT (RRID:SCR_023656) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/SlideSeq_Pipeline/README/

Software pipeline developed in collaboration with BRAIN Initiative Cell Census Network and BRAIN Initiative Cell Atlas Network. Supports processing of spatial transcriptomic data generated with Slide-seq commercialized as Curio Seeker assay.

Proper citation: Slide-seq Pipeline (RRID:SCR_023379) Copy   

•   Source: SciCrunch Registry

http://www.proteomesoftware.com/products/scaffold/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Visualize and validate complex MS/MS proteomics experiments

Proper citation: Scaffold (RRID:SCR_014321) Copy   

•   Source: SciCrunch Registry

https://lookerstudio.google.com/

Former name Google Data Studio, is online tool for converting data into customizable informative reports and dashboards introduced by Google on March 15, 2016 as part of enterprise Google Analytics 360 suite. Online service for graphic data visualization.

Proper citation: Google Looker Studio (RRID:SCR_023549) Copy   

•   Source: SciCrunch Registry

http://www.vsh.com/products/mflt/index.asp

Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software.

Proper citation: ModFit LT (RRID:SCR_016106) Copy   

•   Source: SciCrunch Registry

https://github.com/IGGoncalves/PhysiCOOL

Software Python library tailored to perform model calibration studies with PhysiCell. Generalized framework for model Calibration and Optimization Of modeLing projects.

Proper citation: PhysiCOOL (RRID:SCR_023305) Copy   

•   Source: SciCrunch Registry