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https://www.leica-microsystems.com/products/confocal-microscopes/details/product/leica-hcs-a/

Software supporting Leica Microsystem microscopes by performing high content screening automation. The software combines the flexibility of a point-scanning confocal with the high speed of a camera-based widefield system to compensate for specimen drift, single object tracking and immersion fluid.

Proper citation: Leica HCS A (RRID:SCR_015811) Copy   

•   Source: SciCrunch Registry
  

https://github.com/thackl/cross-species-scaffolding

Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Software that generates in silico mate-pair reads from single-/paired-end reads of your organism of interest, and a closely related reference genome. It can improve draft genomes by using preferred scaffolding software with the newly created read data. Super-scaffolding of draft genome assemblies with in silico mate-pair libraries derived from (closely) related references.

Proper citation: Cross-species scaffolding (RRID:SCR_015932) Copy   

•   Source: SciCrunch Registry
  

Ratings or validation data are available for this resource

https://github.com/garber-lab/ESAT

Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends."

Proper citation: End Sequence Analysis ToolKit (ESAT) (RRID:SCR_015812) Copy   

•   Source: SciCrunch Registry
  

https://compumedicsneuroscan.com/product/synamps-rt-64-channel-eeg-erp-ep-amplifier/

Equipment that is an EEG signal amplifier for 64-channel montages. It is suitable for recording data from high sampling rate (20,000 Hz) Auditory Brain Stem recordings and Spike Spindles to true DC recordings of CNV and P300.

Proper citation: Neuroscan SynAmps RT 64-channel Amplifier (RRID:SCR_015818) Copy   

•   Source: SciCrunch Registry
  

http://microbetracker.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone. Software for bacterial microscopy image analysis. It is designed to detect and outline bacterial cells in microscopy images and to analyze fluorescence signal inside them.

Proper citation: MicrobeTracker (RRID:SCR_015939) Copy   

•   Source: SciCrunch Registry
  

https://github.com/larvalign/larvalign

Software package including computational methods for aligning gene expression patterns from the larval brain of Drosophila melanogaster. Its method includes evaluation of the registration framework involved in template generation and mapping.

Proper citation: larvalign (RRID:SCR_015815) Copy   

•   Source: SciCrunch Registry
  

https://github.com/harry-thorpe/piggy

Pipeline for analyzing intergenic regions in bacteria. It is designed to be used in conjunction with Roary (https://github.com/sanger-pathogens/Roary).

Proper citation: Piggy (RRID:SCR_015941) Copy   

•   Source: SciCrunch Registry
  

https://github.com/KravitzLab/fed/wiki

Flexible open-source device for measuring feeding behavior. FED measures food intake in mice. It is battery powered and designed to be used in rodent colony caging.Home cage-compatible feeding system that measures food intake with high accuracy and temporal resolution. FED offers alternative to commercial feeders, with convenience of use in tradition colony rack caging.

Proper citation: Feeding Experimentation Device project (RRID:SCR_015942) Copy   

•   Source: SciCrunch Registry
  

http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gblocks (RRID:SCR_015945) Copy   

•   Source: SciCrunch Registry
  

http://www.biovoxxel.de/

Software toolkit for analyzing tool for microscopic images. It contains plugins and some macros dealing with image filtering, image segmentation and binary image processing and analysis.

Proper citation: BioVoxxel Toolbox (RRID:SCR_015825) Copy   

•   Source: SciCrunch Registry
  

http://www.treedyn.org/

Visualization software that links unique leaf labels to lists of variables/values pairs of annotations (meta-information), independently of the tree topologies, remaining fully compatible with the basic newick format. These relationships are used by dynamic graphics operators, information visualization methods like Projection, Localization, Labelization, Reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TreeDyn (RRID:SCR_015946) Copy   

•   Source: SciCrunch Registry
  

http://alleninstitute.github.io/dipde/

Simulation platform for numerically solving the time evolution of coupled networks of neuronal populations. DiPDE can facilitate the fast exploration of mesoscale (population-level) network topologies, where large populations of neurons are treated as homogeneous with random fine-scale connectivity.

Proper citation: DiPDE (RRID:SCR_015822) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sanworks

Software for a measurement and control system for behavior research, most often used to implement operant (Go/NoGo, 2AFC) tasks. This software controls a hierarchy of hardware modules, each powered by an Arduino-programmable microcontroller.

Proper citation: Bpod (RRID:SCR_015943) Copy   

•   Source: SciCrunch Registry
  

http://www.genetherapyreview.com/gene-therapy-research

The National Gene Vector Laboratories (NGVL) was established as a cooperative national effort to produce and distribute vectors for human gene transfer studies.

Proper citation: National Gene Vector Laboratories (RRID:SCR_015944) Copy   

•   Source: SciCrunch Registry
  

http://www.fsm.ethz.ch/publications-list/software.html

Software for tracking and analysis based on algorithms describing structural and topological features of fiber-like objects. The program operates on images from any microscopic source (atomic force or transmission electron microscopy, optical, fluorescence, confocal, etc.), acquiring the spatial coordinates of objects.

Proper citation: FiberApp (RRID:SCR_015826) Copy   

•   Source: SciCrunch Registry
  

https://github.com/ABCD-STUDY/geocoding

Software that uses a geo-location database to determine individuals' residential environment in Adolescent Brain Cognitive Development (ABCD) study. It performs queries given individuals' residential history in longitude and latitude.

Proper citation: geocoding (RRID:SCR_016007) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/SC3.html

Software tool for the unsupervised clustering of cells from single cell RNA-Seq experiments. SC3 is capable of identifying subclones from the transcriptomes of neoplastic cells collected from patients.

Proper citation: SC3 (RRID:SCR_015953) Copy   

•   Source: SciCrunch Registry
  

https://github.com/haotianteng/Chiron

Software basecaller for Oxford Nanopore Technologies' sequencers.

Proper citation: Chiron (RRID:SCR_015950) Copy   

•   Source: SciCrunch Registry
  

http://www.hermit-reasoner.com/

Algorithm for a reasoner for ontologies written using the Web Ontology Language (OWL). Given an OWL file, HermiT can determine whether or not the ontology is consistent, identify subsumption relationships between classes, and much more.

Proper citation: HermiT OWL Reasoner (RRID:SCR_016006) Copy   

•   Source: SciCrunch Registry
  

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Center for pathobiology research development.

Proper citation: Emory Epithelial Pathobiology Research Development Center (RRID:SCR_015916) Copy   

•   Source: SciCrunch Registry