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http://scanimage.vidriotechnologies.com/

Open source software application for laser scanning microscopy, electrophysiology, laser scanning photostimulation, and other physiological methods focused on neurobiology. Used to control laser scanning microscopes without need for custom data acquisition hardware. Standard data acquisition boards are used to acquire data and control laser scanning. The tasks of signal integration and image processing are placed on the computer CPU. Multiple versions of ScanImage are available, each with their own features.

Proper citation: ScanImage (RRID:SCR_014307) Copy   

•   Source: SciCrunch Registry

http://bigwww.epfl.ch/thevenaz/turboreg/

An ImageJ plugin for the automatic alignment of a source image (or a stack) to a target image. Manual, automatic, and batch alignment modes are available. Users may specify some landmarks to establish the initial correspondence between images. In automatic and batch modes, the landmarks are automatically refined to match the landmarks of the target image. After registration, the plugin creates a warped image using the final position of the source image and the target landmarks. The plugin can be called by a macro or by another plugin. Technical guidance is available on the website.

Proper citation: TurboReg (RRID:SCR_014308) Copy   

•   Source: SciCrunch Registry

http://actimetrics.com/products/freezeframe/

A video-based system to detect animal movement in fear conditioning experiments, as well as movements in learned helplessness experiments. FreezeFrame can detect animal movements (as small as 1mm) and actions, including grooming, sniffing, turning, and rearing. It can also collect and process data for learned helplessness experiments, such as Tail Suspension and the Porsolt Forced Swim Test. This software can monitor animals for up to 15 times per second.

Proper citation: FreezeFrame (RRID:SCR_014429) Copy   

•   Source: SciCrunch Registry

http://animaltracker.elte.hu/

A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.

Proper citation: AnimalTracker (RRID:SCR_014397) Copy   

•   Source: SciCrunch Registry

http://www.spotimaging.com/software/spot-basic/

Image capture software which creates publication quality images. SPOT allows users to view the live image and a preview of the captured image side by side, enabling image editing before capture. Enhancements such as calibration marks and measurements can be applied after image capture. An advanced version is also available.

Proper citation: SPOT Basic (RRID:SCR_014313) Copy   

•   Source: SciCrunch Registry

http://mastrave.org

A software library written to perform vectorized scientific computing and oriented to ease complex modelling tasks such as those typically needed within environmental models, even when involving irregular and heterogeneous data series. The Mastrave project attempts to allow a more effective, quick interoperability between GNU Octave and Matlab users by using a well documented wrap around the main incompatibilities between those computing environments and by promoting a general idiom based on their common, stable syntagms.

Proper citation: Mastrave modelling library (RRID:SCR_014399) Copy   

•   Source: SciCrunch Registry

http://www.biopac.com/product/acqknowledge-software/

A software program that allows the user to perform data acquistion, stimulation and analyses. Users do not need to know the programming language or a new protocol view. AcqKnowledge Software is compatible with MP150 Research Systems, MP36R Research Systems, and MRI and fMRI Setups. A variety of offline and online analysis tools allows users to customize data recordings and targeted analyses. The software can perform automated analysis routines, output a range of stimulus paradigms, and allows users to record from multiple hardware devices simultaneously.

Proper citation: AcqKnowledge Software (RRID:SCR_014279) Copy   

•   Source: SciCrunch Registry

http://www.objectiveimaging.com/download/software.php

Automated scanning software used in conjunction with the Leica DM6000B microscope to obtain whole-slide image mosaics of histological slides. When performing a scan, Turboscan or the standard scan may be used.

Proper citation: Surveyor with Turboscan (RRID:SCR_014433) Copy   

•   Source: SciCrunch Registry

https://www.rebuildingakidney.org

A consortium of research projects working to optimize approaches for the isolation, expansion, and differentiation of appropriate kidney cell types and their integration into complex structures that replicate human kidney function. Their goal is to coordinate and integrate research to support the development and implementation of strategies such as de novo repair of nephrons, the re-generation of nephrons, and the in vitro engineering of a biological kidney to enhance renal repair and promote the generation of new nephrons in the postnatal organ. Investigators may apply for funding of a kidney-related project through the RBK Partnership Project. Funded projects would join the consortium.

Proper citation: ReBuilding a Kidney (RRID:SCR_014442) Copy   

•   Source: SciCrunch Registry

http://www.ventana.com/documents/ImageViewerBrochure.pdf

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 12,2024. A digital slide image software that is used with the VENTANA iScan Coreo Au slide scanner. This software helps facilitate viewing high quality images with little latency. The image view software can also support the viewing of multiple images simultaneously.

Proper citation: Ventana Image Viewer (RRID:SCR_014446) Copy   

•   Source: SciCrunch Registry

http://www.sandiegoinstruments.com/any-maze-video-tracking/

Video tracking system used to automate testing in a variety of behavioral apparatus. ANY-maze can automatically track the tail, head, or body of a test animal in up to 16 pieces of apparatus. The software can record live images or digital files with different camera types and save the data in multiple formats. ANY-maze contains built in statistical tests and standard measures for distance, speed, mobility, duration, etc., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ANY-maze (RRID:SCR_014289) Copy   

•   Source: SciCrunch Registry

http://www.bio-rad.com/en-us/product/quantity-one-1-d-analysis-software

Software used for Bio-Rad imaging systems to acquire, quantitate, and analyze a variety of data. The software allows automatic configuration of imaging systems with appropriate filters, lasers, LEDs, and other illumination sources. It also contains tools for automated analysis of tests and assays such as 1-D electrophoretic gels, western blots, and colony counts.

Proper citation: Quantity One 1-D Analysis Software (RRID:SCR_014280) Copy   

•   Source: SciCrunch Registry

http://www.definiens.com/research/tissue-studio/developer-xd

A development environment designed to create automated image analysis solutions for segmentation and classification tasks. It delivers quantitative and consistent data for any type of image (e.g., IHC, ISH, IF images in different formats). Developer XD also contains a large library of image analysis algorithms, which users can add to, for whole slide images and tissue microarrays (TMAs). It can be integrated with an existing Tissue Studio installation.

Proper citation: Definiens Developer XD (RRID:SCR_014283) Copy   

•   Source: SciCrunch Registry

http://downloads.thermofisher.com/Instrument_Software/qPCR/Step-1/SOP23_Release%20Notes_4482516.pdf

A software program for the Applied Biosystems StepOne and StepOnePlus Real-Time PCR Systems. StepOne software allows the user to open and analyze experiments generated from either the StepOne or the StepOnePlus system. Users can set up experiments, send experiments to the instrument, control the instrument settings, and collect and analyze data.

Proper citation: StepOne Software (RRID:SCR_014281) Copy   

•   Source: SciCrunch Registry

http://www.agilent.com/en-us/products/cell-analysis-(seahorse)/software-download-for-wave-desktop

Software to manage Seahorse XFe24 Analyzer, which measures OCR and ECAR of live cells in a 24-well plate format. Users can create and modify assay templates and analyze and manage data.

Proper citation: Seahorse Wave (RRID:SCR_014526) Copy   

•   Source: SciCrunch Registry

https://github.com/nickFurlotte/pylmm

A Python package for doing linear mixed model associations in genome wide association studies (GWAS). The software corrects for population structure using EMMA.

Proper citation: pyLMM (RRID:SCR_014525) Copy   

•   Source: SciCrunch Registry

http://www.starrlifesciences.com/products/vitalview-software

A data acquisition and analysis software program. The program collects data from sensors and receivers and displays graphical data analysis as well as descriptive statistics.

Proper citation: VitalView Software (RRID:SCR_014497) Copy   

•   Source: SciCrunch Registry

https://ndar.nih.gov/tools_guid_tool.html

A customized software application that generates a Global Unique Identifier for each study participant. The GUID is a universal subject ID that allows researchers to share data specific to a study participant without exposing personally identifiable information (PII). The GUID has been approved by the NIH Office of General Counsel.

Proper citation: GUID Tool (RRID:SCR_014530) Copy   

•   Source: SciCrunch Registry

https://www.qut.edu.au/research/research-projects/landmark-biobanks

A repository of human tissue samples collected during the LANDMark study (Longitudinal Assessment of Neuropathy in Diabetes using novel ophthalmic markers). The LANDMark Biobank longitudinal dataset contains blood and tissue (skin) samples and matching detailed phenotypic data of three microvascluar complications of type 1 diabetes: neuropathy, nephropathy and retinopathy.

Proper citation: LANDMark BioBanks (RRID:SCR_014534) Copy   

•   Source: SciCrunch Registry

http://www.exploranova.com/products/mercator/

A software package for quantification of histological sections. This software performs functions including: management and analysis of regions of interest, annotations, statistical analysis, and 3D visualization. These results are edited in an Excel-compatible spreadsheet.

Proper citation: Mercator (RRID:SCR_014493) Copy   

•   Source: SciCrunch Registry