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

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

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

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.

Automatic quantification nuclear staining with CellProfiler

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

Website of Turku Bioimaging - Image Data Team (TBI-IDAT) containing our current and past projects as well as software and tools we use.

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.

Some CellProfiler plugins.

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)

“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.

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.

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

Documentation and scripts to install CellProfiler on eddie3

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

slideNormalize: normalisation of histological high-resolution images.