About processing of images captured via cell painting

I have the following doubts when I read papers on cell painting based image profiling assays. As I am new to this topic, please answer to these questions

1)whether the merged image (composite image)is taken as such for further image analysis.I mean the painted colored composite image??

or the negatives of individual cell organelles captured by different filter channels are processed???

3)I could read the process of overlaying images on the top of another to form composite image.In that case is that image 2D or 3D .Does image registration is needed for cell painted images for further image analysis

4)Can we process the images obtained by cell painting using MATLAB

Hello Sreelekshmi @9645451493,

In the Carpenter lab, we typically make measurements on images of the Cell Painting dyes individually – each channel is measured separately. So, no, we don’t make measurements on merged images.

I am not sure what you mean by negatives of individual cell organelles, but as I said above, we do make measurements on the individual channels captured using different filter sets.

We typically overlay the images in such a way that they remain 2D images saved as .png files for quick inspection.

How you process the images is entirely up to you! If you are familiar with Matlab, you could perform data analysis using that program. We like to use CellProfiler to build pipelines that can be reused between experiments and don’t require coding experience. Typically start by illumination correcting all images and then we will build a pipeline that identifies nuclei and cytoplasm and makes measurements for each channel within these compartments. For large scale Cell Painting experiments, we run CellProfiler on Amazon Web Services cloud infrastructure using Distributed CellProfiler: GitHub - CellProfiler/Distributed-CellProfiler: Run encapsulated docker containers with CellProfiler in the Amazon Web Services infrastructure.

I hope this is helpful,
Pearl

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Thank you Madam for this prompt response…this information is really helpful …

Those images obtained from different emission filter channels are first converted into grayscale and then apply illumination correction and other processing methods to segment out major compartments.Right??

We obtain multichannel images where each channel comes from a different filter set and is already a grayscale image (often these images are “pseudo-colored” so that each channel appears a different color, but the colors that are represented are arbitrary). You can read more about this in point #4 of this article. These are the images that we use for illumination correction and then segmentation.

Good luck!

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Thank you for the clarification