cellprofiler

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

A pixel classification based multiplexed image segmentation pipeline

A curated list of awesome cytodata resources

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

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

Image-based Profiling Handbook

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

Running cellprofiler on eddie3 / SGE clusters

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

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

Tools for Processing Results from CellPainting Assay

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

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

“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.

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.

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

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

Collect distributed cellprofiler results into sqlite databases.

Automatic quantification nuclear staining with CellProfiler