cellprofiler

There are 1 repository under cellprofiler topic.

• CellProfiler / CellProfiler-Analyst

  Open-source software for exploring and analyzing large, high-dimensional image-derived data.

  cellprofilercellprofiler-analystimage-analysismachine-learning
  Language:Python 147
• awesome-biological-image-analysis

  hallvaaw / awesome-biological-image-analysis

  A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

  awesomeawesome-listbioimage-analysisbiologycellprofilerimage-analysisimage-processingimagejimagingmicroscopysegmentation
  120

• BodenmillerGroup / ImcSegmentationPipeline

  A pixel classification based multiplexed image segmentation pipeline

  cellprofilerimcpipelinepixel-classificationsegmentationubuntu
  Language:Jupyter Notebook 86

• cytomining / pycytominer

  Python package for processing image-based profiling data

  carpenter-labcytominerimage-processingmicroscopymorphological-profilingway-labpythoncellprofiler
  Language:Python 80

• cytodata / awesome-cytodata

  A curated list of awesome cytodata resources

  awesomeawesome-listcellprofilerimage-analysismachine-learningmorphology
  73

• DistributedScience / Distributed-CellProfiler

  Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.

  cellprofilerdockeraws
  Language:Python 39

• cytomining / profiling-handbook

  Image-based Profiling Handbook

  cytomininghandbookguidemorphological-profilingcellprofiler
  9

• cytomining / CytoTable

  Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

  cellprofilerpythonsingle-cell-analysisway-lab
  Language:Python 7

• broadinstitute / cmQTL

  High-dimensional phenotyping to define the genetic basis of cellular morphology

  morphologyprofilingcellprofilerquantitative-trait-lociprimary-cellscarpenter-lab
  Language:Jupyter Notebook 6
• slideToolKit

  swvanderlaan / slideToolKit

  slideToolkit: a free toolset for analyzing wholeslide high-resolution digital histological images.

  cellprofilerhistologyopenslide
  Language:Shell 5

• Ati-74 / Trackrefiner

  analyzing CellProfiler output

  cellprofilerimage-processingtracking
  Language:Python 4

• CarragherLab / cptools2

  Running cellprofiler on eddie3 / SGE clusters

  biologycellprofilerhpc-clusterimaging-informaticspythonsge
  Language:Python 4

• ome / omero-guide-cellprofiler

  omeroguidecellprofiler
  Language:Jupyter Notebook 4

• WayScience / cellpainting_predicts_cardiac_fibrosis

  Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts

  cell-paintingcellprofilerimage-processingimage-based-analysismachine-learningpycytominer
  Language:Jupyter Notebook 4

• WayScience / JUMP-single-cell

  Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)

  cell-paintingcellprofilerimage-analysisimage-processingpythonpycytominer
  Language:Jupyter Notebook 4
• Nuclear-translocation-analysis

  JoachimGoedhart / Nuclear-translocation-analysis

  Tutorial for single cell analysis of nuclear translocation measured by timelapse imaging

  cell-biologycellprofilerdatavisualizationdatavizimage-processingimage-segmentation
  Language:R 3

• apahl / cellpainting

  Tools for Processing Results from CellPainting Assay

  cellprofilerpandasrdkitnim-lang
  Language:Python 2

• Scotchman0 / CellProfiler_Ubuntu_Installer

  Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6, unet and classify

  cellprofilercellsegmentationclassifypixelsunetdata-analysislinuxpython3ubuntu1804unetwxpython
  Language:Python 2

• pranjaldhole / singularity-cellprofiler

  Singularity-based linux container with CellProfiler 4 pre-installed into it.

  singularity-containerssingularity-hubcellprofilersingularitycontainerstutorial-sourcecode
  Language:Shell 1

• biomicrodev / jonaslab-cpp

  Some CellProfiler plugins.

  bioimage-analysiscellprofiler
  Language:Python 0

• CarragherLab / install_cellprofiler

  Documentation and scripts to install CellProfiler on eddie3

  cellprofiler
  Language:Shell 0

• CarragherLab / meld

  Collect distributed cellprofiler results into sqlite databases.

  cellprofilerdatabase
  Language:Python 0

• CirculatoryHealth / ExpressScan_Glycophorin

  Scripts used for the "Glycophorin C in carotid atherosclerotic plaque reflects intraplaque hemorrhage and pre-procedural neurological symptoms" paper.

  atherosclerosiscellprofilerdigital-pathologyexpressscanplaqueplaque-characteristicslidetoolkitwhole-slide-imaging
  Language:HTML 0

• Clotterdam / Laan-et-al-2023-CellProfiler

  OrganelleProfiler and OrganelleContentProfiler pipelines for CellProfiler as described in Laan et al (PLoS ONE, 2023)

  cell-biologycellprofilercellprofiler-pipelineendothelial-cellsimagingvwfsecretory-pathwayweibel-palade-bodies
  0

• jessievb / automated_CFA

  Automated image analysis of colony formation assay experiments, using Cell profiler and R markdown

  cellprofilerrimage-processingimage-analysis
  Language:HTML 0

• 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.

  cellprofilercellprofiler-pipelinecellprofiler-analysismitotic-cells-segmentationmaximum-intensity-projections
  Language:R 0

• 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.

  cellprofilerilastikinterdiscipinary-teamworkmachine-learningr-programmingshell-scripts
  Language:R 0

• 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.

  pythonfijikerasimage-segmentationimage-processingdockercellprofilerbash-script
  Language:HTML 0

• vatsal-jari / MicroFace.github.io

  traumaticellprofilermicroglial-morphology
  Language:R 0

• apahl / cellpainting2

  Analyzing Cell Painting results with Dask and Pandas - not yet ready for use by others

  cellprofilerdaskjupyter-notebookpandasrdkit
  Language:Python

• apahl / img_viewer

  A plate image viewer for visually analysing Cell Painting results

  golangcellprofilerwebview
  Language:Go

• dirmeier / rnaiutilities

  A collection of python modules and command line tools for processing image-based RNAi screens.

  pythonrnaicellprofilerdatabasesqlitemicroscopy
  Language:Python

• sbamin / CellProfileR

  R scripts to clean/analyse CellProfiler output, forked from

  cellprofilernormalizationpreprocessing
  Language:R

• swvanderlaan / slideNormalize

  slideNormalize: normalisation of histological high-resolution images.

  cellprofilerhistologyslidetoolkit
  Language:C++

• ToledoEM / Pipelines_CellProfiler

  Automatic quantification nuclear staining with CellProfiler

  cellprofilerhow-tohowtopipeline