Automated image analysis of colony formation assay experiments, using Cell profiler and R markdown
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Updated
Jul 6, 2017 - HTML
Automated image analysis of colony formation assay experiments, using Cell profiler and R markdown
Automatic quantification nuclear staining with CellProfiler
Tools for Processing Results from CellPainting Assay
Analyzing Cell Painting results with Dask and Pandas - not yet ready for use by others
A plate image viewer for visually analysing Cell Painting results
A collection of python modules and command line tools for processing image-based RNAi screens.
“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.
Tutorial for single cell analysis of nuclear translocation measured by timelapse imaging
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.
Running cellprofiler on eddie3 / SGE clusters
Install script for CellProfiler v3.1.9 on Ubuntu 18.04.3 LTS(+) - bash, installs python3.6, unet and classify
Collect distributed cellprofiler results into sqlite databases.
Website of Turku Bioimaging - Image Data Team (TBI-IDAT) containing our current and past projects as well as software and tools we use.
Singularity-based linux container with CellProfiler 4 pre-installed into it.
High-dimensional phenotyping to define the genetic basis of cellular morphology
OrganelleProfiler and OrganelleContentProfiler pipelines for CellProfiler as described in Laan et al (PLoS ONE, 2023)
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