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https://www.scionics.com/pyrat_de.html

Software tool for management of animal facility data by Scionics Computer Innovation GmbH. Used by laboratory animal facilities. Used by researchers, animal house managers, animal keepers and others to access their data from same source. Available in English, French, German, Italian, Portuguese and Spanish.

Proper citation: Python based Relational Animal Tracking (RRID:SCR_021014) Copy   

•   Source: SciCrunch Registry

https://www.bmglabtech.com/mars-data-analysis-software/

Proprietary software package for data analysis by BMG Labtech.

Proper citation: MARS Data Analysis Software (RRID:SCR_021015) Copy   

•   Source: SciCrunch Registry

https://neurodatawithoutborders.github.io/matnwb/

Software Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.0 files.

Proper citation: MatNWB (RRID:SCR_021156) Copy   

•   Source: SciCrunch Registry

https://github.com/bahanonu/ciatah

Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.

Proper citation: calciumImagingAnalysis (RRID:SCR_021153) Copy   

•   Source: SciCrunch Registry

https://americanlaboratorytrading.com/lab-equipment-products/innovadyne-technologies-nanodrop-2-pipetting-system_15425

Liquid handling system designed for high precision pipetting.

Proper citation: Innovadyne Technologies: Nanodrop 2 Pipetting System (RRID:SCR_021033) Copy   

•   Source: SciCrunch Registry

https://github.com/NeurodataWithoutBorders/nwb-jupyter-widgets

of widgets for visualization NWB data in Jupyter notebook. Widgets allow you to navigate through hierarchical structure of NWB file and visualize specific data elements. Designed to work with NWB 2.0 files and to be easy to extend.

Proper citation: NWBwidgets (RRID:SCR_021154) Copy   

•   Source: SciCrunch Registry

https://driftage.readthedocs.io/

Software tool as modular multi agent framework to detect concept drifts from batch or streaming data.

Proper citation: Driftage (RRID:SCR_021031) Copy   

•   Source: SciCrunch Registry

https://caiman.readthedocs.io/

Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras.

Proper citation: CaImAn (RRID:SCR_021152) Copy   

•   Source: SciCrunch Registry

https://www.phantomhighspeed.com/products/cameras/mirocnn/c110

Small, sturdy camera with all standard Phantom features and image quality. Memory can be partitioned up to 63 times to deliver images from 1.3 Mpx sensor with 12-bit depth and tightly packed 5.6 micron pixel size. Miro C110 is capable of 1295 fps at 720p HD and up to 52445 fps at reduced resolutions.

Proper citation: Phantom: Miro C110 camera (RRID:SCR_021081) Copy   

•   Source: SciCrunch Registry

https://biospherix.com/c-shuttle/

Oxygen controlled hood for handling cells under physiologic or pathophysiologic conditions. Double door entry allows import/export of materials without perturbation of experimental conditions. Optional control of carbon dioxide as well. Receives C-Chamber Incubator Subchamber to transfer cells without exposure to room air.

Proper citation: BioSpherix: C Shuttle Glove Box hood (RRID:SCR_021082) Copy   

•   Source: SciCrunch Registry

https://cit.kuleuven.be/smart/infrastructure/documents/mcr501.pdf

Stress controlled rheometer.THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 19,2026.

Proper citation: Anton Paar: MCR501 rheometer (RRID:SCR_021122) Copy   

•   Source: SciCrunch Registry

https://github.com/sciensic/SCIGA

Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing.

Proper citation: SCIGA (RRID:SCR_021002) Copy   

•   Source: SciCrunch Registry

https://github.com/tanghaibao/jcvi/wiki/ALLMAPS

Software tool for computing scaffold ordering that maximizes colinearity across collection of maps including genetic, physical or comparative maps into final chromosome build. Robust scaffold ordering based on multiple maps. ALLMAPS is robust against common mapping errors, and generates sequences that are maximally concordant with input maps. Used in building high quality genome assemblies.

Proper citation: ALLMAP (RRID:SCR_021120) Copy   

•   Source: SciCrunch Registry

http://api.brain-map.org/api/v2/structure_graph_download/1.json

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.

Proper citation: Allen Mouse Reference Atlas Ontology (RRID:SCR_021000) Copy   

•   Source: SciCrunch Registry

http://sycamore.h-its.org/sycamore/

Web browser based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Allows database supported modelling, basic model checking and estimation of unknown kinetic parameters based on protein structures. Integrates different online applications as well as locally installed software. Provides user guidance for sequence of steps associated with model building, model checking, simulation and analysis of results.

Proper citation: SYCAMORE (RRID:SCR_021117) Copy   

•   Source: SciCrunch Registry

https://biospherix.com/oxycycler-gt4181cn/

Carbon Monoxide, Nitric Oxide, O2, and CO2 controller with limit control of relative humidity and monitoring of temperature conditions when used in combination with C-Chamber incubator subchamber from BioSpherix. Features secondary monitors for both Carbon Monoxide and Nitric Oxide and may be used in combination with I-Hood Incubator Hood from BioSpherix to ventilate fumes.

Proper citation: BioSpherix: OxyCycler GT4181CN Controller (RRID:SCR_021113) Copy   

•   Source: SciCrunch Registry

https://github.com/tseemann/abricate

Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.

Proper citation: Abricate (RRID:SCR_021093) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenMined/PySyft

Software Python library for secure and private Deep Learning. Decouples private data from model training, using Federated Learning, Differential Privacy, and Encrypted Computation and Homomorphic Encryption within main deep learning frameworks. Used for computing on data you do not own and cannot see.

Proper citation: PySyft (RRID:SCR_021012) Copy   

•   Source: SciCrunch Registry

http://crosslinkviewer.org/

Open source web based visualization tool for exploring crosslinking mass spectrometry results. Displays residue resolution positional information including linkage sites and linked peptides, all types of crosslinking reaction product, ambiguous results and additional sequence information such as domains.

Proper citation: xiNET (RRID:SCR_021010) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/life-science/pcr/real-time-pcr/real-time-pcr-instruments/quantstudio-systems/models/quantstudio-12-flex.html

System can simultaneously run up to four 3072 reaction QuantStudio 12K Flex OpenArray plates in about four hours. When combined with the QuantStudio 12K Flex OpenArray AccuFill System, can produce up to 110000 data points or more in 8 hour day. Has touch screen interface and comprehensive software analysis tools for gene expression, genotyping, and digital PCR increase productivity. Has five interchangable block formats including: OpenArray plate, TaqMan Array card, 384-well, and 96-well (0.1 and 0.2 mL).

Proper citation: Thermo Fisher: Applied Biosystems: QuantStudio 12K Flex RealTime PCR System (RRID:SCR_021098) Copy   

•   Source: SciCrunch Registry