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https://pillow.readthedocs.io/en/stable/

Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool.

Proper citation: pillow (RRID:SCR_023337) Copy   

•   Source: SciCrunch Registry
  

http://openneu.ro/metasearch

Web application search tool intended to help users find MRI data shared publicly on the Web, particularly from projects organized under the 1000 Functional Connectomes Project (FCP) and International Neuroimaging Data-sharing Initiative (INDI). Users can perform queries visually to select a cohort of participants with brain imaging data based on their demographics and phenotypic information and then link out to imaging measures.

Proper citation: MetaSearch (RRID:SCR_014751) Copy   

•   Source: SciCrunch Registry
  

https://github.com/imagej/pyimagej

Software provides set of wrapper functions for integration between ImageJ2 and Python. Supports original ImageJ API and data structures. Used to combine ImageJ and ImageJ2 with other tools available from Python software ecosystem, including NumPy, SciPy, scikit-image, CellProfiler, OpenCV, ITK and many more.

Proper citation: PyImageJ (RRID:SCR_023336) Copy   

•   Source: SciCrunch Registry
  

https://lifesciences.tecan.com/microplate-washers-hydrospeed?p=tab--1

Advanced plate washer, designed for quick, parallel washing of entire 96- and 384-well plates. This avoids time differences between wells for uniform results. Provides full control of wash power for optimized washing of cells, beads and ELISAs. Equipped with 96 and 384 indexing wash head and optimized magnetic carriers.

Proper citation: Tecan: HydroSpeed plate washer (RRID:SCR_023457) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html

Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.

Proper citation: RMassBank (RRID:SCR_002797) Copy   

•   Source: SciCrunch Registry
  

https://github.com/tobiasrausch/alfred

Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.

Proper citation: Alfred (RRID:SCR_023354) Copy   

•   Source: SciCrunch Registry
  

https://github.com/neurobio-hiroshima/WRAQ

Open source microcontroller based system for wheel running activity in mice.Used to track circadian rhythms of rodents using microcontroller, powered by lithium polymer battery, and surveys exercise activity for up to 30 days. Data can be stored on microSD card or using online server using WiFi connection. Python software provides system interface with ActogramJ to analyze chronobiological aspects of data.Repository includes guide for installing integrated developmental environment and dependent libraries for building and setting up WRAQ systems - WRAQ and WRAQ-Wifi. WRAQ and WRAQ-WiFi are based on Adafruit Adalogger and DFRobot FireBeetle ESP32 connected to 4- and 8-bit binary counters receiving signal from reed switch attached to 5-inch flying saucer respectively.

Proper citation: Wheel Running Activity acQuisition (RRID:SCR_023353) Copy   

•   Source: SciCrunch Registry
  

https://awi.cuhk.edu.cn/KinasePhos/download.html

Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool.

Proper citation: KinasePhos 3.0 (RRID:SCR_023595) Copy   

•   Source: SciCrunch Registry
  

https://blobtoolkit.genomehubs.org/blobtools2/

Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.

Proper citation: BlobTools2 (RRID:SCR_023351) Copy   

•   Source: SciCrunch Registry
  

https://github.com/citiususc/BigSeqKit

Software parallel Big Data toolkit to process FASTA and FASTQ files at scale. Used to manipulate FASTA/Q files at scale with speed and scalability at its core.

Proper citation: BigSeqKit (RRID:SCR_023592) Copy   

•   Source: SciCrunch Registry
  

https://www.diagenode.com/en/categories/bioruptor-shearing-device

Sonication system for optimal shearing of biological and chemical samples.

Proper citation: Diagenode: Bioruptor (RRID:SCR_023470) Copy   

•   Source: SciCrunch Registry
  

https://www.licor.com/bio/support/answer-portal/imaging-systems/odyssey-fc.html

System used to image and analyze Western blots. Odyssey Fc imager has been discontinued.

Proper citation: LI-COR: Odyssey Fc Imaging System (RRID:SCR_023227) Copy   

•   Source: SciCrunch Registry
  

https://www.promega.com/resources/software-firmware/glomax-systems/glomax-discover-system-software/

System includes firmware and plate reader software for reading absorbance, fluorescence, or luminescence in 96-well plates.

Proper citation: GloMax Discover System Software and Firmware (RRID:SCR_023469) Copy   

•   Source: SciCrunch Registry
  

https://upsetplot.readthedocs.io/en/stable/

Software Python implementation of UpSet plots to visualize set overlaps.

Proper citation: UpSetPlot (RRID:SCR_023225) Copy   

•   Source: SciCrunch Registry
  

https://www.childrenshospitals.org/content/analytics/product-program/pediatric-health-information-system

Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals.

Proper citation: Children's Hospital Association Pediatric Health Information System (RRID:SCR_023168) Copy   

•   Source: SciCrunch Registry
  

http://blimp.cs.queensu.ca/

Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication.

Proper citation: BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) Copy   

•   Source: SciCrunch Registry
  

https://andor.oxinst.com/products/ixon-emccd-cameras-for-life-science

Scientific camera with EMCCD image sensor that is capable of detecting single photon events without image intensifier, achievable by way of unique electron multiplying structure built into the chip.

Proper citation: Andor: iXon Ultra EMCCD camera (RRID:SCR_023166) Copy   

•   Source: SciCrunch Registry
  

https://andor.oxinst.com/downloads/uploads/Andor_Luca-S_Manual.pdf

Luca-S camera of single photon sensitive imaging Andor family scientific cameras with Electron Multiplying Charge Coupled Device detector, designed for most challenging low-light imaging applications.

Proper citation: Andor: Luca S EMCCD camera (RRID:SCR_023165) Copy   

•   Source: SciCrunch Registry
  

https://www.heka.com/downloads/hardware/manual/m_itc18.pdf

Second generation low noise 16 bit computer interface from Instrutech Corporation. 16-bit Multi-Channel Data Acquisition Interface with PCI or USB host adapter.

Proper citation: Heka Elektronik: InstruTECH ITC-18 (RRID:SCR_023164) Copy   

•   Source: SciCrunch Registry
  

http://www.humanmotorthalamus.com/

A research tool for clinical and experimental neuroscience, which provides images of human thalamus in the stereotactic planes of the coordinate system based on intercommissural line. Images include histological sagittal sections, sagittal maps, coronal maps, horizontal maps, and MRI images all from the same brain. The website also provides materials and methods section, references to the articles and presentations describing research data (on which the maps are based), and a bibliography on the synaptic relationships of subcortical and cortical afferents with projection and local circuit neurons in the motor thalamus.

Proper citation: Human Thalamus in 3D Stereotactic Coordinates (RRID:SCR_014214) Copy   

•   Source: SciCrunch Registry