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https://diagnostics.roche.com/global/en/products/instruments/discovery-xt-research-platform.html
Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing.
Proper citation: Roche: Ventana Discovery XT Immunohistochemistry Processor (RRID:SCR_018643) Copy
Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR.
Proper citation: Thermo Fisher: Arcturus Cellect Laser Capture Microdissection System (RRID:SCR_018641) Copy
Automated wide range incubator used to minimize plate movement, receive samples, store plates, and track plates.Temperature range is from 10 to 50 degrees Celsius with humidity level of up to 95 rH.
Proper citation: Thermo Fisher: Cytomat 6001 Automated Wide Range Incubator (RRID:SCR_018646) Copy
http://www.mediacy.com/imagepro
Software platform to perform image processing, analysis, and data reporting for microscope-based research and quality inspection.
Proper citation: Image Pro (RRID:SCR_016497) Copy
https://www.humancellatlas.org
Software tool as a catalog of comprehensive reference of human cells based on their stable properties, transient features, locations and abundances. Map to show the relationships among its elements. Open data international collaborative project involving diverse scientific communities to provide a framework for understanding cellular dysregulation in human disease.
Proper citation: Human Cell Atlas (RRID:SCR_016530) Copy
https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl
Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.
Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy
Platform for analysis of the genetics of cardiovascular disease.Used for searching and analysis of human genetic information linked to myocardial infarction, atrial fibrillation and related traits while protecting the integrity and confidentiality of the data.
Proper citation: Cardiovascular Disease Knowledge Portal (RRID:SCR_016536) Copy
http://www.ajnr.org/content/25/6/945.long
Software tool written in Java that reads DICOM-files from Dynamic Susceptibility Contrast (DSC) Magnetic Resonance Imaging (MRI) and calculates standardized Time-to-Peak (stdTTP) parameter. Maps from this calculation are provided as RGB- and Monochrom2-Dicom files and may be sent to a PACS automatically. Works on windows® platforms on PC’s (Intel® CPUs from Pentium I up to the I7-octo cores) together with the Philips 1.5T ACS-NT up to the Ingenia Systems (n> 20.000), with the Philips 3.0T Systems (n ~ 1.000), the Siemens 1.5T Avanto (SQ-machine) (n> 10.000) and the Siemens 3.0T TimTrio (n ~ 200) so far. Works with uncompressed DICOM-standard files.
Proper citation: jPerfusionModule (RRID:SCR_016534) Copy
http://www.cyto.purdue.edu/cdroms/micro1/7_spon/vaytek/voxblast.htm
Software application for science and medicine which offers 3-D Measurement, 3-D Volume Visualization, and 3-D Rendering for any 3-D data. It accepts stacks of registered 2-D images and creates 3-D projections from any viewpoint.
Proper citation: VoxBlast (RRID:SCR_016491) Copy
https://doi.org/10.1016/j.neuroimage.2018.07.046
Software package for simulation framework and codes for estimating nonparametric Granger causality. Used to study brain functions.
Proper citation: nonparametricGGC_toolbox (RRID:SCR_016539) Copy
https://github.com/INM-6/NetworkUnit
Library of a test driven framework for formally validating scientific models against experimental data used for validation testing of spiking neuron network simulations on the network activity level.
Proper citation: NetworkUnit (RRID:SCR_016543) Copy
Software as a cross platform application for automating the processing of μCT and OPT image data. Used for standarization of embryo images prior to export to the PhenoDCC. Capable of processing other image modalities and specimens. Can be download as a stand alone release.
Proper citation: HARP (RRID:SCR_016546) Copy
Software tool as a desktop 3D volume viewer. Used for analysing results of automatic phenotype detection from the LAMA pipeline. Developed in Python using QT, and the PyQtGraph.
Proper citation: VPV (RRID:SCR_016545) Copy
https://gitlab.com/danio-code/public/dcc
Software tool as an annotation structure and user-hosted platform for sequencing experiment data, suitable for lab-internal documentation, collaborations and large-scale annotation efforts.
Proper citation: DCC (RRID:SCR_016544) Copy
https://cm.jefferson.edu/rna22/
Software tool as a pattern based algorithm for detecting microRNA binding sites and their corresponding microRNA and mRNA complexes. Allows interactive exploration and visualization of miRNA target predictions. Permits link-out to external expression repositories and databases.
Proper citation: RNA22 (RRID:SCR_016507) Copy
Software application as an integrated web resource of marmoset biological data. Used to find genomic, expression and alternative splicing data to facilitate the study of animal model for neuropsychiatric and social behavior research and to support biological analyses such as functional (ontology) enrichment analysis and protein-protein-network.
Proper citation: CajaDB (RRID:SCR_016506) Copy
https://www.genome.jp/tools/dinies/
Web server for predicting unknown drug-target interaction networks from various types of biological data in the framework of supervised network inference.
Proper citation: DINIES (RRID:SCR_016505) Copy
http://www.compbio.dundee.ac.uk/jpred/
Software tool for protein secondary structure prediction from the amino acid sequence by the JNet algorithm. Makes also predictions on Solvent Accessibility and Coiled-coil regions.
Proper citation: Jpred (RRID:SCR_016504) Copy
Software application as an open source Pyton library to search and predict miRNA targets.
Proper citation: miRmap (RRID:SCR_016508) Copy
https://www.janelia.org/open-science/mimms-10-2016
Modular platform for performing two‐photon laser scanning microscopy (TPLSM) optimized for in vivo applications.
Proper citation: MIMMS microscope 1.0 (2016) (RRID:SCR_016511) Copy
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