Introduction to the BBBC021 dataset

Last updated on 2026-03-31 | Edit this page

Overview

Questions

  • What is the BBBC021 dataset?

Objectives

  • Get an overview of the research question behind BBBC021.
  • Understand the file structure.

The example dataset BBBC021

Welcome! For the next exercise we will use a compact, well-studied image set pulled from the Broad Bioimage Benchmark Collection (BBBC). The collection we are using is BBBC021, which contains images of MCF7 breast cancer cells treated with a panel of compounds. You can browse the full dataset here: https://bbbc.broadinstitute.org/BBBC021.

Why this dataset? Firstly, it is real experimental data used to discover which compounds change cell morphology and to cluster compounds by the pathways they perturb. Secondly, it is small and clean enough for hands-on learning, but biologically rich, so the analyses you build here translate to real research problems.

What did the experiment involve?

  • Cells: MCF7 (human breast cancer cell line)
  • Perturbations: 112 small molecules + DMSO control at multiple concentrations (we will use just two wells for the workshop)
  • Stains (channels):
    • DAPI: stains DNA / nuclei (channel1)
    • Phalloidin: stains f‑actin (channel2)
    • Anti‑β‑tubulin antibody: stains microtubules (channel3)

In this workshop, we will focus on comparing cells treated with DMSO to those treated with cytochalasin D (cytoD). It is a classic actin‑disrupting drug. When actin polymerization is disrupted you often see cells lose their spread morphology, change shape, and show altered phalloidin signal. That makes this a great case study for image‑based phenotyping.

Challenge

Challenge

Given what you know about the dataset so far, can you formulate a research question? Try thinking about questions we may be able to answer using the images.

One option is: does cytochalasin D induce a morphological change in MCF7 cells?

But note that other questions may be interesting too! For example: does cytoD induce cell death?

Files and Metadata

Filenames contain the experimental metadata so you do not need a separate spreadsheet. For example, the file name cytoD_B07_s1_channel1.tif can be read as

  • Treatment: cytoD
  • Well: B07
  • Site: s1 (image field within the well)
  • Channel: channel1 (DAPI in this dataset)

Downloading sample data

If you have not yet done so, you will need to download the dataset now. Click on the button below and unzip the archive to a convenient location on your computer.

Download dataset

Next steps

Ready to build the analysis pipeline? Proceed to the next section to open these images in CellProfiler and start measuring the features that will answer our question.

Key Points
  • BBBC021 is a high-content imaging dataset of MCF7 cells.
  • File names contain information about treatments and experimental parameters.