Example of implementation in multi-channel microscopy images

[gwaybio]

Hi @yfukai - thanks for your pointers in #65.

I'm writing here with a separate question about an example pipeline using multi-channel images. Do you know of any examples? Could you point us to a tutorial?

Thanks! Greg

[yfukai]

Hi, thanks @gwaybio for your interest! We simply expect the users to apply the correction independently to each channel. If we find good example images, we will add them to the tutorial.

[gwaybio]

Thanks for your quick reply @yfukai - This makes sense. I might also be able to contribute a tutorial if we get to this before you.

One additional quick clarification: I just want to make sure that I clarify that I meant static (not time-lapse) multi-channel images (e.g. from the Cell Painting assay). Does the same answer apply here? (Sorry for not being clear in my original question!)

[yfukai]

Thanks for that! The contribution is also highly welcome. The difference between the time-lapse and non-time-lapse images is only whether we correct the baseline drift or not (for non-time-lapse images (typically mosaic multi-pos images), the package does not correct the baseline as it can be affected by spatial sample density etc.) In that sense, I would say we expect the same for the static images.

[donovanr]

I've been trying to run some cell painting data through BasSiCPy as documented in #104 and was wondering if anyone (@gwaybio @jenna-tomkinson ?) has a reproducible example that runs on the current dev or main branch of the code to analyze and correct a set of static images?

[gwaybio]

It looks like #104 is working off of the develop branch implementation? Here is one of our examples using the main implementation: https://github.com/WayScience/NF1_SchwannCell_data/tree/main/1_preprocessing_data