Tools   Select Another Resource Report Type

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://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://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/google-deepmind/deepmind-research/tree/master/enformer

Software package provides implementation of the Enformer model and examples on running the model.

Proper citation: Enformer (RRID:SCR_024805) 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://github.com/kundajelab/tfmodisco

Software application as algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data.

Proper citation: TF-Modisco (RRID:SCR_024811) Copy   

•   Source: SciCrunch Registry

https://data.scilifelab.se

Platform collates tools, databases, information, and other resources that can be useful to researchers and data producing facilities working in the area of data driven life science. Hub for data driven life science research in Sweden.

Proper citation: SciLifeLab Data Platform (RRID:SCR_024865) 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://github.com/arduino/Arduino

Open-source physical computing platform based on I/O board and development environment that implements the Processing/Wiring language. Arduino can be used to develop stand-alone interactive objects or can be connected to software on your computer.

Proper citation: Arduino IDE (RRID:SCR_024884) 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.graham-center.org/maps-data-tools/social-deprivation-index.html

SDI is composite measure of area level deprivation based on seven demographic characteristics collected in the American Community Survey and used to quantify the socio-economic variation in health outcomes.

Proper citation: Social Deprivation Index (RRID:SCR_025026) Copy   

•   Source: SciCrunch Registry

https://github.com/dattalab/moseq2-app

Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time.

Proper citation: moseq2-app (RRID:SCR_025031) 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://sites.google.com/site/plaresmedima/

Software tool to support translation of basic research in medical image analysis into early clinical studies.

Proper citation: PMI (RRID:SCR_025084) Copy   

•   Source: SciCrunch Registry

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

Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets.

Proper citation: Fslutils (RRID:SCR_024943) 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