How to generate "feature_1_frame_1_p1_dsDNA" in example data

[nolanlab]

How to generate "feature_1_frame_1_p1_dsDNA" in example data

[BokaiZhu]

Hi, the detial can be found here in the paper, but in brief, it was generated from DeepCell, as a probability map of predicted nuclues location.

[StiThor]

Hi again. I seem to have trouble finding the script for generating a similar file as the one mentioned above with my own data. I have IMC data and I run the Steinbock segmentation (Deepcell/Mesmer) from Bodenmiller to make the cell mask. However, this approach does not generate the necessary file needed to do the REDSEA. Could you link that particular part of the script in Deepcell needed to make the file?

[BokaiZhu]

Hi there I see the question here. The short answer is the method is not yet compatible with the segmentation you are using here. The Redsea method we described in the manuscript works on an earlier version of Deepcell (described ref1 and ref2): where Deepcell will produce a nuclear probability map instead of directly a whole cell seg map. We then use the nuclear prob map to run a watershed algo (here), and generate boundary pixels like this (where Redsea runs on the red pixels)

While the current segmentation you are using will directly produce a label map, and the potential boundary map would look like something:

As you can tell, they look slightly different and might cause some problems for the code, partially discussed here.

We do have a working script that is compatible with these newer versions of segmentation map, but we do need some time before we can be confident enough that is safe to use before we release it. For now, I will make this issue open and happy to discuss further.

[StiThor]

I see :) Very exciting that you guys are working with something that works with the newer version of Deepcell since our experience is that this segmentation works quite well! Have you thought of trying to have the REDSEA built in the code for Steinbock Deepcell so the whole process could be automated? If you need some Guiney pigs to test these new scripts on that are compatible with the newer version of deepcell I`m your guy :)

[janinemelsen]

Hi! I was wondering whether there is any update on using REDSEA in combination with the current mesmer segmentation:)