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https://github.com/liufan-creat/bulkGAN

Software tool for scRNA and spatial transcriptomics.Used to generate RNA data close to real bulk RNA-seq with constraints of scRNA-seq data, based on keras and tensflow framework.

Proper citation: bulkGAN (RRID:SCR_024798) Copy   

•   Source: SciCrunch Registry

https://www.adobe.com/ca/products/fresco.html

Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support.

Proper citation: Adobe Fresco (RRID:SCR_024887) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST

Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction.

Proper citation: FMRIB's Automated Segmentation Tool (RRID:SCR_024920) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/SGAE

Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics.

Proper citation: SGAE (RRID:SCR_024803) Copy   

•   Source: SciCrunch Registry

https://github.com/qt-creator/qt-creator?tab=readme-ov-file

Cross-platform, complete Integrated Development Environment for application developers to create applications for multiple desktop, embedded, and mobile device platforms, such as Android and iOS. It is available for Linux, macOS and Windows operating systems. In addition, you can use the experimental WebAssembly plugin to build applications in web format and run them in web browsers.

Proper citation: Qt Creator (RRID:SCR_024883) Copy   

•   Source: SciCrunch Registry

https://www.3dhistech.com/research/software-downloads/

Software tool for working with whole slide images. Digital microscope application for supporting histopathological diagnostic workflow and microscope examination process. Advanced slide viewing software used in clinical pathology and research.

Proper citation: 3DHISTECH SlideViewer (RRID:SCR_024885) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MELODIC

Software tool to use at both the subject and group level to decompose FMRI data into time courses and spatial maps using Independent Component Analysis. Used to decompose single or multiple 4D data sets into different spatial and temporal components.

Proper citation: Multivariate Exploratory Linear Optimized Decomposition into Independent Components (RRID:SCR_024916) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FABBER

Software command-line tool for approximate Bayesian inference using generative signal models.

Proper citation: FABBER (RRID:SCR_024917) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/verbena

Software tool for quantification of perfusion and other haemodynamic parameters from Dynamic Susceptibility Contrast perfusion MRI of the brain.

Proper citation: VERBENA (RRID:SCR_024919) Copy   

•   Source: SciCrunch Registry

https://biostat.app.vumc.org/wiki/Main/PowerSampleSize

Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size.

Proper citation: PS:Power and Sample Size Calculation (RRID:SCR_024912) Copy   

•   Source: SciCrunch Registry

https://www.gehealthcare.com/products/bone-and-metabolic-health/prodigy

System offers dual energy X-ray absorptiometry assessment. Bone densitometry scan with enCORE v18 software platform. Meets International Society for Clinical Densitometry testing guidelines. Used to take measurements to work out the strength of bones in advanced bone and metabolic health clinical applications.

Proper citation: GE: Healthcare: Lunar Prodigy Advance system (RRID:SCR_025004) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/baycest

Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra.

Proper citation: BayCEST (RRID:SCR_024951) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery

Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask.

Proper citation: Atlasquery (RRID:SCR_024944) Copy   

•   Source: SciCrunch Registry

https://github.com/BlankenbergLab/gmxtras/tree/main

Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files.

Proper citation: GROMACS topology editors (RRID:SCR_025013) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT

Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another.

Proper citation: FNIRT (RRID:SCR_024923) Copy   

•   Source: SciCrunch Registry

https://support.qmenta.com/knowledge/sienax-2.6-/-fsl-6.0

Software tool to estimate total brain tissue volume, from single image, normalized for skull size.

Proper citation: SIENAX (RRID:SCR_024926) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster

Software application used to form clusters, report information about clusters and/or perform cluster based inference.

Proper citation: fsl-cluster (RRID:SCR_024938) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise

Software tool for nonparametric permutation inference on neuroimaging data.

Proper citation: randomise (RRID:SCR_024937) Copy   

•   Source: SciCrunch Registry

https://www.3ds.com/products/simulia/abaqus

Software suite for finite element analysis and computer aided engineering.

Proper citation: Abaqus FEA (RRID:SCR_024997) Copy   

•   Source: SciCrunch Registry