Human Hepatocyte and Murine Fibroblast cells – Co-culture experiment

Accession number BBBC026 · Version 1

Biological application

This 384-well plate has images of co-cultured hepatocytes and fibroblasts. Every other well is populated (A01, A03, ..., C01, C03, ...) such that 96 wells comprise the data. Each well has 9 sites and thus 9 images associated, totaling 864 images.


For each well there is one field and a single image nuclear image (Hoecsht). Images are in 8-bit PNG format. (402 MB)


CellProfiler version 2015_08_05 (Windows, 64-bit, git hash aa38cd9)

CellProfiler Analyst version 2014_04_01 (Windows, 64-bit)

ilastik version 0.5.12 (Windows, 64-bit)

CellProfiler version 2015_11_20 - Used for Ground Truth pipelines (Windows, 64-bit) (Needed to fix a bug in FilterObjects)

CellProfiler pipelines

CellProfiler pipeline before Cellprofiler Analyst ('Previous Workflow')

CellProfiler pipeline after ilastik ('New Workflow')

CellProfiler pipeline to compare ground truth to CP+CPA pipeline

CellProfiler pipeline to compare ground truth to ilastik+CP pipeline

ilastik Project

ilastik Project file

Ground truth 

The images in column '01' have 4000 hepatocytes per well. These can be considered as 'negative' controls. The wells are specified in the filename.

The images in column '23' have 9500 hepatocytes per well. These can be considered as 'positive' controls. The wells are specified in the filename.

Hand-annotated Ground Truth Images

As described in section 2.4 of the paper noted below (Logan), 5 images were manually annotated with cell type. For each nucleus a colored seed point is given. Red seeds denote hepatocyte cells, green seeds denote fibroblast cells, and blue seeds denote other cell types.

These images are used in the CellProfiler pipelines comparing the performance of the two different workflows. (4.6 MB)

To replicate Figure 4 (in the article below)

Run these Matlab scripts

Run this script, which wraps the second.

Second script

Further instructions on how to configure are in the comments.

Published results using this image set

Logan DJ, Shan J, Bhatia SN, Carpenter AE (2015). Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods pii: S1046-2023(15)30170-5 / doi. PMID: 26687239. PMCID: PMC4766037. (Research article)


Creative Commons LicenseThe BBBC026v1 image set are licensed under a Creative Commons Attribution 3.0 Unported License by Anne Carpenter and David Logan.