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jnkather avatar jnkather commented on August 29, 2024 1

QuPath is open source: https://qupath.github.io

from msifromhe.

YoniSchirris avatar YoniSchirris commented on August 29, 2024

@jnkather same here, is it possible to add this function?

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jnkather avatar jnkather commented on August 29, 2024

thank you for your interest, please find the function below! However I recommend you use our latest version at https://github.com/jnkather/DeepHistology. In that version, we use QuPath to process the whole slide images which makes that function obsolete.

% JN Kather, extract microns per pixel MPP from Leica SVS
% if extraction fails, use rescue image
function currMPP = Info2MPPrescue(currImInfo,channel,rescuePath, rescueFileName)

    sq = @(varargin) cell2mat(varargin);
    
    currMPP = Info2MPP(currImInfo,channel);
    
    if isempty(currMPP) || isnan(currMPP)
        disp(['starting MPP rescue attempt for file name: ',rescueFileName]);
       % try to rescue
       targetFile = dir([rescuePath,rescueFileName,'*.svs']);
       if numel(targetFile)==1
           
            newInfo = imfinfo([rescuePath,targetFile(1).name]);
            [~,ni] = sort(sq(newInfo.Width));
            currMPP = Info2MPP(newInfo,ni(end));
            
       else
           disp(['rescue attempt FAILED (code 1), target files = ',num2str(numel(targetFile))]);
       end

    end
    
   
end

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YoniSchirris avatar YoniSchirris commented on August 29, 2024

Many thanks. I'll look at your latest version. Would you know from the top of your head approximately how long it takes to tesselate a single WSI? I'm checking some benchmarks

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jnkather avatar jnkather commented on August 29, 2024

about 1-2 minutes per WSI

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YoniSchirris avatar YoniSchirris commented on August 29, 2024

Am I correct that qupath is proprietary software? As then it's still worthwhile to do the tessellation using available matlab/python code.

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