nolanlab/redsea

redsea's Issues

Masks & multichannel transform

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.

Introduction of NaN when cells don't border other cells

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

Do you have plan for Python implementation

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!

.fcs output

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?

No License in Repo

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.

Running matlab with example data

Hi,

Why do I get an error with "rgb_image = MibiGetRGBimageFromMat(nucLm,maxv)" running the script in MATLAB?

How to generate "feature_1_frame_1_p1_dsDNA" in example data

How was the MIBI feature_1_frame_1_p1_dsDNA file generated?