Pipelines for analyzing BBBC021 data set



I’m interested in analyzing images from BBBC, specifically the set of MCF7 cells (BBBC021, https://data.broadinstitute.org/bbbc/BBBC021/). There was a set of pipelines for normalizing image intensity, segmenting cells, and extracting features provided for the original paper in Journal of Biomedical Screening, 2013 (http://pubs.broadinstitute.org/ljosa_jbiomolscreen_2013/). However, these pipelines look to be from CP1.0.

Are updated versions of these pipelines available? It would be great to use these pipelines to ensure I’m performing intensity normalization and segmentation properly, as I would like to do so some subsequent analysis with the segmented cells. Others have the BBBC021 data set in recent publications for image analysis, so I’m hoping that such a pipeline might be available somewhere.

Thanks for any help!


Hi @bchidest! Please try out this pipeline.

analysis.cppipe (27.2 KB)

illum.cppipe (12.4 KB)


Hi @karhohs, this is exactly what I was hoping for, thanks!


Can @Ackerman post those to the BBBC page?


Yes @Anne_Carpenter, I can do this!