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Hi, Bokai
Would you mind share some scripts for generating segmentationParams.mat file from a masks tiff file and multichannel tiff to single channel tiff ? Make it easier to using downsteam boundary compensation.
Thx.
Hi,
first: thanks for releasing the code here!
I have tested the scripts on our data and found a potential issue when individual cells are not directly neighbouring other cells. As far as I understand, here you calculate the total boundary as the sum of boundaries to neighbouring cells. In cases where cells are not in direct contact with other cells, the sum is 0. Next, here boundary length is divided by 0, introducing NaN
which propagates to the summation here filling the normalized data matrix with NaN
. One fix might be to set cellPairNorm(isnan(cellPairNorm)) = 0;
after line 56. I hope I didn't miss anything.
Thanks!
Nils
Thanks for developing this signal correction method. It is definitely essential for multiplexed imaging analysis.
I noticed that the code currently is only in MATLAB and I was wondering if there is a plan for Python implementation. Many thanks!
Hi,
Super cool that you guys have developed this algorithm for spillover correction of signals for this type of data. Trying to run the Jupyter script, and it seems to be working fine. But I would like to get the output as .fcs files for downstream analysis. How can I do that?
Hello yunhaoBai and BokaiZhu!
There is no license in the repository and was wondering if that was an oversight -- technically no license means that no one can legally use / modify the code here -- although that seems directly contrary to your intentions and your communications here about RedSEA.
As I'd talked with you in a separate issue, I've been making (and now have made) a python script for integrating this algorithm with steinbock in a separate fork of RedSEA, but I'm happy to take it down if you don't want versions of your repo being made.
How was the MIBI feature_1_frame_1_p1_dsDNA file generated?
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