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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Rainin: Pipet-Lite LTS Pipette L-1000XLS+ Resource Report Resource Website |
Rainin: Pipet-Lite LTS Pipette L-1000XLS+ (RRID:SCR_023894) | instrument resource | Pipet-Lite™ XLS+ manual single-channel pipette, 100-1000 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-1000XLS+) | Pipette, 100 ul to 1000 ul, instrument, equipment, Rainin | Restricted | SCR_023894 | Pipet-Lite LTS Pipette L-1000XLS+ | 2026-08-29 11:28:31 | 0 | ||||||||||
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Rainin: Pipet-Lite LTS Pipette L-200XLS+ Resource Report Resource Website |
Rainin: Pipet-Lite LTS Pipette L-200XLS+ (RRID:SCR_023892) | instrument resource | Pipet-Lite™ XLS+ manual single-channel pipette, 20-200 μL, uses LTS™ LiteTouch™ tips. Accurate and precise, ergonomic, autoclavable liquid end, rugged and durable (L-200XLS+) | Pipette, 20 ul to 200 ul, instrument, equipment, manual single channel pipette, Rainin | Restricted | SCR_023892 | , Pipet-Lite™ XLS+, Rainin Pipet-Lite™ XLS+ | 2026-08-29 11:28:04 | 0 | ||||||||||
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Nikon: N-SIM S Super Resolution Microscope Resource Report Resource Website |
Nikon: N-SIM S Super Resolution Microscope (RRID:SCR_023803) | instrument resource | Microscope enables super solution imaging of live cells at ten times the speed of conventional SIM. Powered by ECLIPSE Ti2-E Inverted Research Microscope, taking advantage of its advanced optics, stability and features. | Nikon, live cells imaging, imaging, USEDit | is listed by: USEDit | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023803.pdf | SCR_023803 | N-SIM S Super Resolution Microscope | 2026-08-29 11:28:23 | 0 | ||||||||
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Hitachi: 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL Resource Report Resource Website 1+ mentions |
Hitachi: 16-bit 3-CCD color camera HV-F203GV / HV-F203SCL (RRID:SCR_023888) | instrument resource | High resolution 1/1.8" 3 CCD Progressive Scan Color Camera with 1600 x 1200 pixel (UXGA) that is installed in the ZEISS Axioscan Z1 slide scanner. Integrated functions include electronic shutter from 1/30s to 1/100000s, Long term Integration up to 4s, AGC, external Trigger, Auto Shading, 6 Colour Masking, Frame-On-Demand Function, White Balance, AGC, Black Level Adjustment and Partial Scan Function. | Hitachi, CCD color camera, bright color, camera, instrument, equipment | is related to: Zeiss: Axio Scan.Z1 Slide Scanner | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023888.pdf | SCR_023888 | HV-F203GV / HV-F203SCL camera | 2026-08-29 11:28:24 | 1 | ||||||||
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Cytiva: Biacore 4000 Resource Report Resource Website 1+ mentions |
Cytiva: Biacore 4000 (RRID:SCR_023766) | instrument resource | High throughput Surface Plasmon Resonance system with high quality interaction data for better informed decision making in antibody selection, drug discovery and more., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | USEDit, Cytiva, surface plasmon resonance, | THIS RESOURCE IS NO LONGER IN SERVICE | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023766.pdf | SCR_023766 | , Biacore 4000, Biacore™ 4000 surface plasmon resonance system, Biacore TM 4000 | 2026-08-29 11:28:30 | 1 | |||||||||
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Molecular Devices: SpectraMax iD3 multi-mode microplate reader Resource Report Resource Website 10+ mentions |
Molecular Devices: SpectraMax iD3 multi-mode microplate reader (RRID:SCR_023920) | instrument resource | Microplate reader to measure absorbance, fluorescence and luminescence. | Microplate reader, measure absorbance, measure fluorescence, measure luminescence, | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023920 | SCR_023920 | Molecular Devices SpectraMax iD3 multi-mode microplate reader, SpectraMax® iD3 multi-mode microplate reader | 2026-08-29 11:28:31 | 17 | |||||||||
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caftools Resource Report Resource Website |
caftools (RRID:SCR_023982) | software resource | Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site. | is listed by: Debian | Free, Available for download, Freely available | OMICS_24974 | https://sources.debian.org/src/caftools/ | SCR_023982 | 2026-08-29 11:28:32 | 0 | |||||||||
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BOLT-LMM Resource Report Resource Website 1+ mentions |
BOLT-LMM (RRID:SCR_023978) | data analysis software, data processing software, software application, software resource | Software statistical tool for identifying genetic associations. Used for genome wide association studies in large cohorts. | statistical tool, identifying genetic associations, genome wide association studies, large cohorts, | is listed by: Debian | PMID:25642633 | Free, Available for download, Freely available | OMICS_13504 | https://sources.debian.org/src/bolt-lmm/ | SCR_023978 | bolt-lmm | 2026-08-29 11:28:25 | 2 | ||||||
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QUINT Resource Report Resource Website 1+ mentions |
QUINT (RRID:SCR_023856) | data processing software, software application, software resource, workflow software | Software workflow includes suite of various software to form analysis pipeline of atlas-based quantifuication of labbeled features in histological images from mouse or rat brain. This workflow also suggests and explains with instructional videos the way these software work together. Used for quantification and spatial analysis of labelling in series of rodent brain section images based on available 3D reference atlases. | Allen Common Coordinate Framework, labelling quantification and spatial analysis, analysis pipeline of atlas based quantifuication of labbeled features, histological images, mouse brain, rat brain, images, brain section images, 3D reference atlases, |
is used by: WebNutil is related to: Allen Institute for Brain Science is related to: SeriesZoom has parent organization: University of Oslo; Oslo; Norway |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:31849633 | Free, Freely available | SCR_023856 | 2026-08-29 11:28:31 | 5 | ||||||||
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Brainreg-segment Resource Report Resource Website 1+ mentions |
Brainreg-segment (RRID:SCR_023853) | data processing software, image analysis software, segmentation software, software application, software resource | Software tool for manual segmentation of regions/objects within the brain. Brainreg-segment will only work if the user registers their data with brainreg first. Used for segmentation of 3D shapes in common anatomical space. | Allen Mouse Brain Atlas, Allen Human Brain Atlas, brain imaging, regions segmentation, objects segmentation, segmentation within the brain, | is related to: Allen Institute for Brain Science | Free, Available for download, Freely available | SCR_023853 | 2026-08-29 11:28:04 | 5 | ||||||||||
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CONTRAfold Resource Report Resource Website 1+ mentions |
CONTRAfold (RRID:SCR_023994) | CONTRAfold | simulation software, software application, software resource | Software novel secondary structure prediction method based on conditional log-linear models, a flexible class of probabilistic models which generalize upon SCFGs by using discriminative training and feature-rich scoring. Used for sequence prediction. | sequence prediction, | is listed by: Debian | PMID:16873527 | Free, Available for download, Freely available | OMICS_03452 | https://sources.debian.org/src/CONTRAfold/ | SCR_023994 | CONditional TRAining for RNA Secondary Structure Prediction, contrafold | 2026-08-29 11:28:06 | 2 | |||||
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Conquest DICOM Resource Report Resource Website |
Conquest DICOM (RRID:SCR_023993) | softwre application | Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation. | DICOM training and testing, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/conquest/ | SCR_023993 | conquest-common, conquest-dbase, conquest-postgres, conquest-dicom-server, conquest-sqlite, conquest-mysql | 2026-08-29 11:28:32 | 0 | ||||||||
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miRCode Resource Report Resource Website 100+ mentions |
miRCode (RRID:SCR_023870) | software resource, web application | Web tool for transcriptome wide microRNA target prediction including lncRNAs.Used for whole transcriptome human microRNA target predictions based on the comprehensive GENCODE gene annotation, including long non-coding RNA genes. Coding genes are also covered, including atypical regions such as 5'UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan. Site conservation is aluated based on 46 vertebrates species.Map of putative microRNA target sites in the long non-coding transcriptome. | microRNA target sites, target prediction, transcriptome wide microRNA target prediction, lncRNAs, whole transcriptome human microRNA, | has parent organization: University of California at Santa Cruz; California; USA | Assar Gabrielsson Foundation ; Lars Hierta Memorial Foundation ; Magnus Bergvall Foundation ; Swedish Medical Research Council |
PMID:22718787 | Free, Freely available | SCR_023870 | 2026-08-29 11:28:04 | 187 | ||||||||
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Immunedeconv Resource Report Resource Website 10+ mentions |
Immunedeconv (RRID:SCR_023869) | data analysis software, data processing software, software application, software resource | Software R package for unified access to computational methods for estimating immune cell fractions from bulk RNA sequencing data. | computational methods access, estimating immune cell fractions, bulk RNA sequencing data, | PMID:32124323 | Free, Available for download, Freely available | SCR_023869 | 2026-08-29 11:28:31 | 13 | ||||||||||
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CodonW Resource Report Resource Website 100+ mentions |
CodonW (RRID:SCR_023989) | data analysis software, data processing software, software application, software resource | Software tool designed to simplify Multivariate analysis (correspondence analysis) of codon and amino acid usage. It also calculates standard indices of codon usage. | Multivariate analysis, correspondence analysis, codon and amino acid usage, calculate standard indices, codon usage, | is listed by: Debian | Free, Available for download, Freely available | OMICS_08756 | https://sources.debian.org/src/codonw/ | SCR_023989 | codonw | 2026-08-29 11:28:05 | 322 | |||||||
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CHIME Resource Report Resource Website |
CHIME (RRID:SCR_023987) | softwre application | Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation. | providing estimates, capacity planning, | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/chime/ | SCR_023987 | COVID-19 Hospital Impact Model for Epidemics, chime | 2026-08-29 11:28:25 | 0 | ||||||||
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NanoString: CosMx Spatial Molecular Imager Resource Report Resource Website 10+ mentions |
NanoString: CosMx Spatial Molecular Imager (RRID:SCR_023909) | instrument resource | Integrated system with mature cyclic fluorescent in situ hybridization chemistry, resolution imaging readout, interactive data analysis and visualization software. Analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded and fresh frozen tissue samples at cellular and subcellular resolution. CosMx SMI enables rapid quantification and visualization of up to 1,000 RNA and 64 validated protein analytes. Spatial single-cell imaging platform that drives deeper insights for cell atlasing, tissue phenotyping, cell-cell interactions, cellular processes, and biomarker discovery. | Spatial single-cell imaging platform, nanoString, spatial molecular imager, molecular imager, formalin-fixed paraffin-embedded samples, fresh frozen tissue samples, cellular and subcellular resolution, | is related to: NanoString Technologies | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023909.pdf | SCR_023909 | CosMx Spatial Molecular Imager, NanoString CosMx Spatial Molecular Imager | 2026-08-29 11:28:31 | 18 | ||||||||
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SunCollect MALDI Sprayer Resource Report Resource Website |
SunCollect MALDI Sprayer (RRID:SCR_023907) | instrument resource | For tissue preparation for Imaging MALDI. The sprayer can handle fresh-frozen or FFPE tissue sections. Enzymes such as trypsin can be applied to the tissue for in situ digestion. Sprayer offers the following key features: Automated delivery of matrix, enzyme or derivatization solutions; 6 port PEEK valve with low dead-volume to minimise liquid usage; Automatic self-cleaning function at end of matrix application; 100 % biocompatible; Compact unit 36 x 49 x 40 cm (w,d,h);Preprogrammed spray protocols;Up to 8 sample slides can be sprayed simultaneously;Easy to use software. | SunChrom Wissenschaftliche Geräte GmbH, SunChrom, Tissue Preparation, | is related to: SunChrom | Restricted | SCR_023907 | SunCollect Sprayer | 2026-08-29 11:28:31 | 0 | |||||||||
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SunChrom: SunCollect CF Spotter Resource Report Resource Website |
SunChrom: SunCollect CF Spotter (RRID:SCR_023906) | instrument resource | CF-Spotter for MALDI-TOF microbial identification. Enables fast, efficient and reproducible sample preparation for MALDI-TOF microbial identification system and relieves your laboratory staff from tedious and time-consuming pipetting. Due to the non-contact application of the solutions, there is no carryover of the samples and the costs for consumables such as pipette tips are eliminated. | SunChrom Wissenschaftliche Geräte GmbH, SunChrom, MALDI-TOF microbial identification system, microbial identification, instrument, equipment | is related to: SunChrom | Restricted | SCR_023906 | CF-Spotter for MALDI-TOF Microbial Identification | 2026-08-29 11:28:05 | 0 | |||||||||
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SunChrom: SunDigest Incubator Resource Report Resource Website |
SunChrom: SunDigest Incubator (RRID:SCR_023905) | instrument resource | SunDigest incubation device provides fully software controlled and highly reproducible digestion process under standardized conditions. Feature includes Temperatures precisely adjustable between 4 °C and 50 °C; On-Tissue digestion process under optimal humidity; Preservation of spatial resolution; High performance digestion at 50 °C; Full digestion process control.Essential for reproducible results. | SunChrom Wissenschaftliche Geräte GmbH, SunChrom, incubator, incubator software controlled, standardized conditions, instrument, equipment | is related to: SunChrom | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_023905.pdf | SCR_023905 | 2026-08-29 11:28:24 | 0 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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