Showing 5 of total 5 results (show query)
cytomining
cytominer:Methods for Image-Based Cell Profiling
`cytominer` is a suite of common functions used to process high-dimensional readouts from image-based cell profiling experiments.
Maintained by Shantanu Singh. Last updated 2 years ago.
50 stars 6.89 score 44 scripts
bioc
flowcatchR:Tools to analyze in vivo microscopy imaging data focused on tracking flowing blood cells
flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.
Maintained by Federico Marini. Last updated 3 months ago.
softwarevisualizationcellbiologyclassificationinfrastructureguishinyappsbioconductorfluorescencemicroscopyparticlestracking
4 stars 5.62 score 8 scripts
gitdemont
IFC:Tools for Imaging Flow Cytometry
Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®' 'Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata/>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Maintained by Yohann Demont. Last updated 27 days ago.
cytometrycytometry-dataflowflow-cytometryflow-cytometry-analysisflow-cytometry-dataflow-cytometry-filesifcimageimaging-flow-cytometryimaging-flow-cytometry-datamicroscopycpp
4 stars 5.34 score 12 scripts
bioimaginggroup
bioimagetools:Tools for Microscopy Imaging
Tools for 3D imaging, mostly for biology/microscopy. Read and write TIFF stacks. Functions for segmentation, filtering and analyzing 3D point patterns.
Maintained by Volker Schmid. Last updated 3 years ago.
4 stars 5.30 score 33 scripts 1 dependents
zcolburn
Bioi:Biological Image Analysis
Single linkage clustering and connected component analyses are often performed on biological images. 'Bioi' provides a set of functions for performing these tasks. This functionality is implemented in several key functions that can extend to from 1 to many dimensions. The single linkage clustering method implemented here can be used on n-dimensional data sets, while connected component analyses are limited to 3 or fewer dimensions.
Maintained by Zachary Colburn. Last updated 5 years ago.
biological-data-analysisbiologycellcppimage-analysismicroscopycpp
3.81 score 13 scripts