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https://www.bdbiosciences.com/documents/15_cellquest_prosoft_analysis.pdf

A software for acquiring and analyzing flow cytometry data. The user can create plots with elements like regions, gates, statistics, markers, and annotated text. The software can also be used for batch analysis or quality control of analysis. Results can be exported and saved., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BD CellQuest Pro (RRID:SCR_014489) Copy   

•   Source: SciCrunch Registry

http://www.evolution.rdg.ac.uk/BayesTraits.html

A computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. It incorporates earlier programs including Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a discrete number of states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, ancestral states and correlations among pairs of traits., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BayesTraits (RRID:SCR_014487) Copy   

•   Source: SciCrunch Registry

http://www.scied.com/pr_cmbas.htm

A software system to assist with cloning simulation, enzyme operations, and graphic map drawing. Clone Manager can also be used as a way to view or edit sequence files, find open reading frames, translate genes, or find genes or text in files. Clone Manager Professional is an upgraded version of Clone Manager Basic., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Clone Manager Software (RRID:SCR_014521) Copy   

•   Source: SciCrunch Registry

http://www.freepascal.org

Free Pascal is a 32, 64 and 16 bit professional Object Pascal compiler targeting multiple processor architectures and operating systems. Documentation, including guides and manuals, are available on the website.

Proper citation: Free Pascal Compiler (RRID:SCR_014360) Copy   

•   Source: SciCrunch Registry

http://aleasol.ch/cms/index.php/clickjoint.en.html

A software for analyzing animal movement on videos and images. The user can define the animal's joints so the software can analyze using a tracking algorithm.

Proper citation: Clickjoint (RRID:SCR_014482) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://www.nikoninstruments.com/Products/Software

Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: NIS-Elements (RRID:SCR_014329) Copy   

•   Source: SciCrunch Registry

https://www.imagescience.de/imagic.html

An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules.

Proper citation: IMAGIC (RRID:SCR_014447) Copy   

•   Source: SciCrunch Registry

http://www.amtimaging.com/www11/english/product_e.html

AMT camera system software that performs digital image acquisition, processing, and storage. An operations manual and software specifications are available on the main site.

Proper citation: AMT Image Capture Software (RRID:SCR_014333) Copy   

•   Source: SciCrunch Registry

http://www.macrogen.com/

A company that provides a variety of next generation sequencing services. The company provides researchers with whole genome resequencing, exome sequencing, targeted sequencing, transcriptomics, and epigenome sequencing.

Proper citation: Macrogen (RRID:SCR_014454) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/index.html

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

Proper citation: SCRATCH (RRID:SCR_014291) Copy   

•   Source: SciCrunch Registry

http://www.biobserve.com/products/viewer/

Software that provides subject tracking with body axis alignment and angle of view, which is then used to track body, nose and tail movements without marking the animal. Users may create the scoring system used by the software, as well as zones to observe, quantify, and compare the behavior of an animal in one or more areas. The software features several data acquisition and analysis tools to gather and interpret the data.

Proper citation: Biobserve Viewer (RRID:SCR_014337) Copy   

•   Source: SciCrunch Registry

http://www.andor.com/scientific-software/iq-live-cell-imaging-software

A live cell imaging software that allows for control of iXon EMCCD and sCMOS cameras in synchronized combination with a number of additional imaging hardware devices. iQ can be used to run experiments to investigate dynamic processes in both single cells and multicellular systems, image fixed samples, and generate 3 dimensional image volumes for analysis.

Proper citation: Andor iQ (RRID:SCR_014461) Copy   

•   Source: SciCrunch Registry

http://g6g-softwaredirectory.com/bio/cross-omics/biomarker/20241BrukerClinProTools.php

Biomarker detection and evaluation software which provides an advanced basis for mining unknown potential biomarkers in complex protein profiles. Visualization tools such as stack plots and box-and-whiskers plots can be used to interactively inspect and compare large data sets originating from samples that contain different clinical diagnoses. ClinProTools also supplies sophisticated mathematical algorithms for the discovery of complex biomarker pattern models. Besides validation, class-prediction tools are also integrated to allow the implementation of the whole biomarker detection and evaluation process.

Proper citation: ClinProTools (RRID:SCR_014341) Copy   

•   Source: SciCrunch Registry

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://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