BBBC013 dataset: U2OS cytoplasm to nucleus translocation (FKHR-GFP)

What it is

A translocation assay: when the drug acts, FKHR-EGFP moves from the cytoplasm into the nucleus. Imaged on an IN Cell Analyzer 3000 with its Trafficking Data Analysis Module.

Files

• BBBC013_v1_images_frm.zip, BBBC013_v1_images_bmp.zip
• BBBC013_v1_platemap_all.txt, BBBC013_v1_platemap_wortmannin.txt, BBBC013_v1_platemap_ly294002.txt
• BBBC013_reproduce_logan.zip (5.4 MB), CellProfiler pipelines and metadata to reproduce the published analysis

Browse it in DataTorch

Dataset · datatorch/translocation-bbbc013 · 192 files

U2OS FKHR-GFP translocation (BBBC013)

Cytoplasm-to-nucleus translocation assay from the Broad Bioimage Benchmark Collection (BBBC013v1). 192 fluorescence microscopy images (640 x 640, 8-bit BMP) from one 96-well plate of human U2OS cells: 96 wells x 2 channels (channel 1 FKHR-GFP, channel 2 DNA stained with DRAQ), one field per well. The plate holds four replicate 9-point dose series of the PI3K inhibitors wortmannin (rows A-D, nM) and LY294002 (rows E-H, uM) plus 8 negative-control and 8 positive-control wells (150 nM wortmannin). Ground truth is the platemap: well, drug, dose and control role are stored as file metadata on every image and the control role is also an image-level label (negative-control, positive-control, dose). The two channels of each well are separate files paired through metadata and folder path; there are no cell outlines. License: CC BY 3.0 (Ilya Ravkin). Source: https://bbbc.broadinstitute.org/BBBC013. Please cite: We used image set BBBC013v1 provided by Ilya Ravkin, available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012].

Open →

The hosted copy holds the whole 8-bit BMP set: 192 images, 96 wells in two channels, one field per well. The platemap travels with the images, so you never have to join a text file by hand:

• Drug, dose and well are stored as metadata on every image. Filter by drug or dose to pull one curve, or one concentration across the replicates.
• Control role is also an image-level label with three values: negative-control (16 images, 8 wells), positive-control (16 images, 8 wells) and dose (160 images, 80 wells).
• The two channels of a well are separate files, paired through their metadata and folder path. There are no cell outlines, so this is a dose-response and classification set, not a segmentation one.

One difference from the platemap file: for wells E01 to H01 the hosted copy follows the metadata in BBBC013_reproduce_logan.zip, which marks them as Wortmannin controls. The platemap file's original value for those four wells is kept in a platemap_dose field, so both readings are there.

What people use it for

Checking that a translocation measure (nuclear over cytoplasmic GFP) gives a clean dose response, and comparing assay quality across methods.

Source and citation

Source: https://bbbc.broadinstitute.org/BBBC013 (read 2026-10-22, license re-checked 2026-10-29). Cite: "We used image set BBBC013v1 provided by Ilya Ravkin, available from the Broad Bioimage Benchmark Collection [Ljosa et al., Nature Methods, 2012]."