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https://github.com/MontpellierRessourcesImagerie/imagej_macros_and_scripts/wiki/Intensity-Ratio-Nuclei-Cytoplasm-Tool

Software tool to calculate ratio of intensity in nuclei and cytoplasm. It needs two images as input cytoplasm channel and nuclei channel.

Proper citation: Intensity Ratio Nuclei Cytoplasm Tool (RRID:SCR_018573) Copy   

•   Source: SciCrunch Registry

https://pubmed.ncbi.nlm.nih.gov/25172804/

Probe uses semi permeable membrane with pore size of 30 kDa which enables small hydrophilic compounds from brain extracellular space to diffuse passively into perfusate. Used to measure extracellular ACh level and glucose metabolites directly without purification.

Proper citation: Custom made 30 kDa microdialysis probe (RRID:SCR_018571) Copy   

•   Source: SciCrunch Registry

https://noblis.org/bioportal/tools.html

Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes.

Proper citation: BioVelocity (RRID:SCR_018501) Copy   

•   Source: SciCrunch Registry

https://www.ttuhsc.edu/pharmacy/research/documents/Amnis-Imagestream-Manual.pdf

Bench top multispectral imaging flow cytometer designed for the acquisition of up to 12 channels of cellular imagery. It combines per cell information with statistical significance of sample sizes of standard flow cytometry.

Proper citation: Luminex: Amnis ImageStreamX Mk II System (RRID:SCR_018589) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/reprocontainers/

Software containerized environments for reproducible neuroimaging. Part of ReproNim - Center for Reproducible Neuroimaging Computation. DataLad dataset with collection of popular computational tools provided within ready to use containerized environments.

Proper citation: ReproNim/containers (RRID:SCR_018467) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/pod/Bio::CUA

Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.

Proper citation: Codon Usage Analyzer (RRID:SCR_018500) Copy   

•   Source: SciCrunch Registry

https://github.com/xiaeryu/SpoTyping-v2.0

Software tool for fast and accurate in silico Mycobacterium spoligotyping from sequence reads.

Proper citation: SpoTyping (RRID:SCR_018466) Copy   

•   Source: SciCrunch Registry

https://omictools.com/bisogenet-tool

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process.

Proper citation: BisoGenet (RRID:SCR_018502) Copy   

•   Source: SciCrunch Registry

http://www.limef.com/Downloads/752-752M%20manual.pdf

Vibrating microtome manufactured by Campden Instruments. 752 Vibroslice tissue cutter for manual tissue transport.

Proper citation: Campden Instruments: Vibroslice vibrating microtome (RRID:SCR_018460) Copy   

•   Source: SciCrunch Registry

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018581.pdfhttp://www.bio-medicine.org/biology-products/Fujifilm-FLA-5100-from-FUJIFILM--Life-Science-1727-1/

EImaging scanner that images fluorescent and radioisotopic samples. It can be used for protein electrophoresis, genomics array analysis, fluorescence, radioisotope detection, and chemiluminescence detection by direct detection method.

Proper citation: Fujifilm: FLA-5100 Scanner (RRID:SCR_018581) Copy   

•   Source: SciCrunch Registry

https://www.illumina.com/documents/products/datasheets/datasheet_cbot.pdf

Genetic amplifier that uses amplification to create single molecule DNA templates and dispense reagents. It also controls reaction times, flow rates, and temperatures.

Proper citation: Illumina: cBot Genetic Amplifier (RRID:SCR_018580) Copy   

•   Source: SciCrunch Registry

https://www.kentscientific.com/products/coda-high-throughput-system/

CODA mouse rat tail-cuff system was designed to allow accurate blood pressure measurement in mice and rats. Blood pressure is measured in the tail of the mouse or rat using Volume Pressure Recording (VPR) sensor technology. Using the included software allows you to continuously view data in real-time.

Proper citation: Kent Scientific: Coda Blood Pressure System (RRID:SCR_018585) Copy   

•   Source: SciCrunch Registry

http://www.bx.psu.edu/miller_lab/dist/README.lastz-1.02.00/README.lastz-1.02.00a.html#install

Software package for sequence alignment. Pairwise aligner for aligning DNA sequences. Designed to handle sequences size of human chromosomes and from different species. Useful for sequences produced by NGS sequencing technologies.

Proper citation: LASTZ (RRID:SCR_018556) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/cs/library/brochures/5990-5596EN.pdf

Agilent 3100 OFFGEL Fractionator performs isoelectric focusing of proteins or peptides in immobilized pH gradient (IPG) gel strips.

Proper citation: Agilent: 3100 OFFGEL Fractionator (RRID:SCR_018433) Copy   

•   Source: SciCrunch Registry

https://mobile.labwrench.com/equipment/8044/applied-biosystems/voyager-de-pro

Benchtop MALDI TOF mass spectrometer that has linear and reflector analyzer. It is used to analyze organic and inorganic compounds, protein identification, synthetic peptide validation, and polymer analysis.

Proper citation: Thermo Fisher: Applied Biosystems: ABI Voyager DE Pro MALDI-Mass Spectrometer (RRID:SCR_018432) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/minimap2

Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences.

Proper citation: Minimap2 (RRID:SCR_018550) Copy   

•   Source: SciCrunch Registry

http://nanotomy.org/

Large scale electron microscopy datasets. Large scale electron microscopy database for Human Type 1 Diabetes.

Proper citation: Nanotomy (RRID:SCR_018565) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/timezone1/

Software package to detect footprints of positive selection for functionally adaptive point mutations in microbial genomes.

Proper citation: TimeZone (RRID:SCR_018564) Copy   

•   Source: SciCrunch Registry

http://doriclenses.com/life-sciences/software/955-doric-neuroscience-studio.html

Software tool which allows to control Doric hardware and acquire all required data simultaneously. Incorporates different modules for each devices connected.

Proper citation: Doric Neuroscience Studio (RRID:SCR_018569) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/ggtree/

Software R package for visualization and annotation of phylogenetic trees with their covariates and other tree like structures with their annotation data. Can import evolutionary data from different tree file formats and analysis programs as well as other associated data from experiments so that various sources and types of data can be displayed on tree for comparison and further analyses.

Proper citation: ggtree (RRID:SCR_018560) Copy   

•   Source: SciCrunch Registry