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https://stoeltingco.com/Neuroscience/Open-Field~9839

Specialized laboratory enclosure used in behavioral neuroscience to assess exploratory behavior, general locomotor activity, and anxiety-related responses in rodents like mice and rats.

Proper citation: Stoeling Co: Open Field Box (RRID:SCR_028738) Copy   

•   Source: SciCrunch Registry

https://med-associates.com/product/behavioral-test-packages-for-mouse/

Laboratory testing system used by scientists to study animal behavior, learning, and addiction. Also known as a "Skinner box," it features levers, lights, sound generators, and food or water dispensers.

Proper citation: Med Associates: Operant Chamber (RRID:SCR_028739) Copy   

•   Source: SciCrunch Registry

https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_028736.pdf

XY-axis Locomotor Activity Chamber (part of Photobeam Activity System or PAS Open Field) is used to track, measure, and analyze the physical movements and behavior of small laboratory animals like mice and rats.

Proper citation: San Diego Instruments: XY-axis Locomotor Activity Chamber (RRID:SCR_028736) Copy   

•   Source: SciCrunch Registry

https://deepneo.co.kr/

Webserver for predicting immunogenic neoantigens. Used to identify immunogenic neoepitopes by capturing the structural properties of peptide-MHC pairs with T cell reactivity.

Proper citation: DeepNeo (RRID:SCR_028672) Copy   

•   Source: SciCrunch Registry

https://www.menarinisiliconbiosystems.com

Biotechnology and diagnostics company specializing in "liquid biopsy" technologies to detect and isolate rare cells like circulating tumor cells (CTCs) from blood or tissue samples. They provide precise single-cell analysis tools used in cancer research and personalized medicine. Offers commercial rare-cell laboratory service providing CD138-positive immunomagnetic enrichment of plasma cells from peripheral blood and immunofluorescence-based plasma-cell identification and enumeration, delivering an enriched circulating multiple myeloma cell fraction for downstream analysis.

Proper citation: Menarini Silicon Biosystems Inc (RRID:SCR_028704) Copy   

•   Source: SciCrunch Registry

https://www.agilent.com/store/productDetail.jsp?catalogId=2010064AA

Benchtop flow cytometer used to analyze and count individual cells or particles. Flow cytometer with 3 lasers (488, 405, 640 nm) and up 14 colors. 6 colors from violet laser; 5 colors from blue laser; 3 colors from red laser. NovoExpress software used for acquisition.

Proper citation: Agilent: NovoCyte 3005 Flow Cytometer (RRID:SCR_028708) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-systems/orbitrap-lc-ms/orbitrap-astral-mass-spectrometer.html?erpType=Global_E1

Mass spectrometer for advanced, high-speed, and deep-coverage biological research, specifically targeting proteomics, clinical biomarker discovery, and single-cell analysis. It combines high-resolution accuracy with a rapid scan speed of up to 200 Hz. Powered by the synergy of the high resolution quadrupole mass filter, Thermo Scientific™ Orbitrap™ mass analyzer and the novel Thermo Scientific™ Astral™ mass analyzer. The combination of these three mass analyzers enables the acquisition of quality high resolution accurate mass (HRAM) data with high sensitivity and dynamic range.

Proper citation: Thermo Scientific: Orbitrap Astral Mass Spectrometer (RRID:SCR_028684) Copy   

•   Source: SciCrunch Registry

https://www.datasci.com/products/software/finepointe-software/finepointe-new-features

Software for collecting, analyzing, and reporting life science data. Used to control inhalation exposure systems, track real-time animal respiration, and calculate precise delivered drug doses in pre-clinical research. It automates aerosol delivery, monitors lung function data, and manages experimental protocols.

Proper citation: Buxco FinePointe Inhalation Software (RRID:SCR_028683) Copy   

•   Source: SciCrunch Registry

https://www.diagenode.com/en/p/bioruptorpico2

Ultrasonic shearing instrument used to fragment chromatin, shear DNA and RNA, and lyse cells.

Proper citation: Diagenode: Bioruptor Pico sonicator (RRID:SCR_028774) Copy   

•   Source: SciCrunch Registry

http://www.mainehealth.org/

Health care organization in Maine, serving communities across Maine and New Hampshire. Includes MaineHealth Institute for Research to support research at MaineHealth ranging from basic laboratory-based research through translational research, which works to apply basic discoveries to medical problems, to clinical research, which studies the direct application of new drugs, devices and treatment protocols to patients, to health services research which seeks to use research methods to help improve and evaluate health care delivery programs and new technologies.

Proper citation: MaineHealth; Portland; United States (RRID:SCR_028781) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/DrugSim2DR/

Software R package to predict drug functional similarity to drug repurposing.

Proper citation: DrugSim2DR (RRID:SCR_024564) Copy   

•   Source: SciCrunch Registry

http://www.jsps.go.jp/english/

Research and outreach organization dedicated to promoting science, research and education. The society has four main objectives, including building international cooperative networks, enhancing education and research at universities, building evidence-based science-promotion systems and creating diverse world level knowledge.

Proper citation: Japan Society for the Promotion of Science (RRID:SCR_001085) Copy   

•   Source: SciCrunch Registry

https://github.com/chaoszhang/A-pro

Software tool for species tree reconstruction from multi-copy gene family trees.Used for estimating unrooted species tree given set of unrooted gene trees and is statistically consistent under the multi-species coalescent model. ASTRAL-pro extends ASTRAL to allow multi-copy genes. ASTRAL-Pro 2, ultrafast and memory efficient version of ASTRAL-Pro that adopts placement based optimization algorithm for significantly better scalability without sacrificing accuracy.

Proper citation: ASTRAL-Pro (RRID:SCR_024520) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/CpGassoc/index.html

Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

Proper citation: CpGassoc (RRID:SCR_000320) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapE15_5_01.htm

Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint E15 Atlas (RRID:SCR_002786) Copy   

•   Source: SciCrunch Registry

http://cmbn-approd01.uio.no/zoomgen/hippocampus/home.do

An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored. Features * Alphabetical and hierarchical overview of 18 hippocampal structures * Detailed, illustrated descriptions of 63 boundaries * Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin * Triple image viewer in which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. Re-use of data from this repository is allowed provided that reference is given to the publication.

Proper citation: Rat Hippocampus Atlas (RRID:SCR_005552) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/sri24/

An MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.

Proper citation: SRI24 Atlas: Normal Adult Brain Anatomy (RRID:SCR_002551) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapP7_01.htm

Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint P7 Atlas (RRID:SCR_002787) Copy   

•   Source: SciCrunch Registry

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

Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.

Proper citation: UNC Human Brain Atlas (RRID:SCR_002606) Copy   

•   Source: SciCrunch Registry