cellprofiler
There are 36 repositories under cellprofiler topic.
CellProfiler/CellProfiler-Analyst
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
hallvaaw/awesome-biological-image-analysis
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
BodenmillerGroup/ImcSegmentationPipeline
A pixel classification based multiplexed image segmentation pipeline
cytomining/pycytominer
Python package for processing image-based profiling data
cytodata/awesome-cytodata
A curated list of awesome cytodata resources
DistributedScience/Distributed-CellProfiler
Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.
cytomining/profiling-handbook
Image-based Profiling Handbook
cytomining/CytoTable
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
broadinstitute/cmQTL
High-dimensional phenotyping to define the genetic basis of cellular morphology
swvanderlaan/slideToolKit
slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.
Ati-74/Trackrefiner
analyzing CellProfiler output
CarragherLab/cptools2
Running cellprofiler on eddie3 / SGE clusters
WayScience/cellpainting_predicts_cardiac_fibrosis
Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts
WayScience/JUMP-single-cell
Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
JoachimGoedhart/Nuclear-translocation-analysis
Tutorial for single cell analysis of nuclear translocation measured by timelapse imaging
apahl/cellpainting
Tools for Processing Results from CellPainting Assay
Scotchman0/CellProfiler_Ubuntu_Installer
Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6, unet and classify
ajdavies73/H2B_FUCCI2a-Nucleus-Segmentation-and-Cell-Cycle-Analysis
CellProfiler pipeline and ImageJ workflow developed for segmentation of H2B_FUCCI2a_MCF7 cell nuclei for per-nucleus and background fluorescence intensity measurement. Example workflows for downstream cell cycle analysis are also provided in this repository.
pranjaldhole/singularity-cellprofiler
Singularity-based linux container with CellProfiler 4 pre-installed into it.
biomicrodev/jonaslab-cpp
Some CellProfiler plugins.
CarragherLab/install_cellprofiler
Documentation and scripts to install CellProfiler on eddie3
CarragherLab/meld
Collect distributed cellprofiler results into sqlite databases.
CirculatoryHealth/ExpressScan_Glycophorin
Scripts used for the "Glycophorin C in carotid atherosclerotic plaque reflects intraplaque hemorrhage and pre-procedural neurological symptoms" paper.
Clotterdam/Laan-et-al-2023-CellProfiler
OrganelleProfiler and OrganelleContentProfiler pipelines for CellProfiler as described in Laan et al (PLoS ONE, 2023)
jessievb/automated_CFA
Automated image analysis of colony formation assay experiments, using Cell profiler and R markdown
radee2k/CellProfiler-analysis-of-reproductive-stress-in-HCT116-
ImageJ macros for preparation of single images from stacks with maximum intensity projections and partially automated selection of slices in focus. CellProfiler Pipeline for yH2AX and 53BP1 counting and mitotic cells segmentation in asynchronous cultures. R scripts for processing of CellProfiler output.
RichardBekoe/Marker_Distribution
“Novel Marker Distribution Pipeline for Analysis of Cell Based Quantitative Spatial Information”. The aim of this research was to analyse quantitative spatial information and provide intuitive visualisation relating to the identification of cells relative to tissue structure and pathology such as cancer tumour.
Turku-BioImaging/turku-bioimaging.github.io
Website of Turku Bioimaging - Image Data Team (TBI-IDAT) containing our current and past projects as well as software and tools we use.
apahl/cellpainting2
Analyzing Cell Painting results with Dask and Pandas - not yet ready for use by others
apahl/img_viewer
A plate image viewer for visually analysing Cell Painting results
dirmeier/rnaiutilities
A collection of python modules and command line tools for processing image-based RNAi screens.
sbamin/CellProfileR
R scripts to clean/analyse CellProfiler output, forked from
swvanderlaan/slideNormalize
slideNormalize: normalisation of histological high-resolution images.
ToledoEM/Pipelines_CellProfiler
Automatic quantification nuclear staining with CellProfiler