Cell Painting Feature extraction

I am from Electrical Engineering and completely new with CellProfiler. At the moment, I have to calculate the Cell Painting Feature mentioned in this https://github.com/carpenterlab/2016_bray_natprot/wiki/What-do-Cell-Painting-features-mean%3F. There are 1783 features mentioned: https://raw.githubusercontent.com/wiki/carpenterlab/2016_bray_natprot/attachments/feature_names.txt

I wonder if there is a available completed way to run a single script that can extract these 1783 features from a group of 5 channels of fluorescent images.

Any help would be appreciated.


Hi Thanh

I am also working on performing feature extraction, but am not part of the Carpenter / Broad team.

For this you would need the raw images and the Cell Profiler pipelines, which is also available in the supporting info. The features are then extracted in Cell Profiler using the Analysis pipeline. For larger amounts of data you need a MySQL-server setup (perhaps just locally) to which the features are written. They are produced in a per-cell fashion, which means that they need aggregation to per-well profiles if you wish to do that.

You probably also need Cell Profiler analyst to review the results of the quality control (quality control pipeline) and also if you wish to evaluate the per-cell data directly output from Cell Profiler (eg. DNA integrated intensity).

Hi EsbenSv,

Thanks for your response,

By reading more carefully on the paper: “Cell Painting, a high-content image-based assay
for morphological profiling using multiplexed fluorescent dyes”, I have nothing more than just follow the steps on the instruction, and it mentioned what you said. However, I encounter another issue that I do not have any experience before which is about MySQL to export to database at step 5g. I am digging in some tutorial about MySQL but still figuring out that needed to go over this step. I am a new user so I could not attached the instruction file. But It was mentioned as “Text S1” in the paper.

Thank you again for your guild.

Hi Thanh

You need to install a MySQL server, which can be done locally. Download link here: https://dev.mysql.com/downloads/mysql/

I would recommend installing the Workspace as well, as this gives you a graphical interface for browsing databases and tables.
I would recommend looking for some MySQL tutorials by google-searching, they will provide you with the basic commands and setups of a MySQL database.