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SchapiroLabor / histoCAT

Histology Topography Cytometry Analysis Toolbox
https://SchapiroLabor.github.io/histoCAT/
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Error during PhenoGraph calculation #91

Open maxgrigori opened 3 years ago

maxgrigori commented 3 years ago

Hello,

I have run into a repeating problem when trying to analyze my IMC data via PhenoGraph, as the necessary step prior to neighbourhood analysis. When running PhenoGraph with e.g. k=30 I get ~30 clusters, of which the first 5-7 clusters show a "cross-shape" with incredibly high values when overlaid with a tSNE (Screenshot attached below). When exporting the .csv-files of these clusters, it shows that incredibly high marker intensities have been calculated (2nd screenshot attached). The rest of the resulting clusters appear to be calculated normally and are also projected normally.
Unfortunately, the subsequent neighbourhood analysis fails - citing "Error while evaluating Menu Callback" later.

During the calculation of the PhenoGraph itself no error is given. (I'll cite the cmd-progress report below anyways, maybe there is something suspicious?) Otherwise I am using histoCAT 1.76 on a Windows10 system.

What may cause the issue and how could it be solved?

I'd be very grateful for your help! Thank You and have a nice day! Best, Max

PS: Finding 30 nearest neighbors... Building Jaccard Graph... 10 percent complete: 3.89 s 20 percent complete: 7.65 s 30 percent complete: 11.41 s 40 percent complete: 15.14 s 50 percent complete: 18.86 s 60 percent complete: 23.06 s 70 percent complete: 26.77 s 80 percent complete: 30.59 s 90 percent complete: 34.49 s 100 percent complete: 38.29 s Finished Jaccard graph in 38.29 s Edge number pruned from 1.26296e+07 to 1.06504e+07 Sparsity: 5.38549e-05 Writing graph to .bin file Percent done: 10 20 30 40 50 60 70 80 90 100 Finished writing .bin file in 192.18 s In windows.. MATLAB: calling convert: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\convert.exe -i C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.bin -o C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights MATLAB: running community detection, ITERATION 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 3 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 5 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 6 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 7 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 8 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 9 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 3 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 10 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 11 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 12 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 3 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 13 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 14 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 15 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 16 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 3 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 17 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 18 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 19 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: running community detection, ITERATION 20 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\community.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.bin -l -1 -v -w C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G_graph.weights > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: modularity scores: C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree

MATLAB: max level is 4 MATLAB: importing level 1 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 1 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 2 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 2 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 3 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 3 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp MATLAB: importing level 4 C:\Users\Maxim\AppData\Local\Temp\Maxim\mcrCache8.4\histoC0\histoCAT\3rdParty\PhenoGraph\Louvain_d\hierarchy.exe C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tree -l 4 > C:\Users\Maxim\Documents\IMCAnalysis\20201117_Analysis_allBiopsies\custom_gates_0\G.tmp Warning: File 'G.tmp' not found.

In LouvainfromBin_Windows>cleanup at 109 In LouvainfromBin_Windows at 82 In phenograph at 73 In Run_Phenograph_Callback at 37 In analyze_button_Callback at 80 In gui_mainfcn at 95 In histoCAT at 42 In @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject)) Warning: File 'G.tree' not found. In LouvainfromBin_Windows>cleanup at 109 In LouvainfromBin_Windows at 82 In phenograph at 73 In Run_Phenograph_Callback at 37 In analyze_button_Callback at 80 In gui_mainfcn at 95 In histoCAT at 42 In @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject)) Warning: File 'G_graph.weights' not found. In LouvainfromBin_Windows>cleanup at 109 In LouvainfromBin_Windows at 82 In phenograph at 73 In Run_Phenograph_Callback at 37 In analyze_button_Callback at 80 In gui_mainfcn at 95 In histoCAT at 42 In @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject)) Warning: File 'G.bin' not found. In LouvainfromBin_Windows>cleanup at 109 In LouvainfromBin_Windows at 82 In phenograph at 73 In Run_Phenograph_Callback at 37 In analyze_button_Callback at 80 In gui_mainfcn at 95 In histoCAT at 42 In @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject)) Warning: File 'G_graph.bin' not found. In LouvainfromBin_Windows>cleanup at 109 In LouvainfromBin_Windows at 82 In phenograph at 73 In Run_Phenograph_Callback at 37 In analyze_button_Callback at 80 In gui_mainfcn at 95 In histoCAT at 42 In @(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject)) assigning random number for current Phenograph File loaded: 0.244004s Allocated space for data: 0.41388s Read data into session: 0.583132s File loaded: 0.153685s Allocated space for data: 0.111081s Read data into session: 0.446758s [...] File loaded: 0.0928287s Allocated space for data: 0.0894717s Read data into session: 0.552152s Phenograph clusters are stored as fcs files in custom_gates_0...

Screenshot 2021-05-20 195334 Screenshot 2021-05-20 195443

DenisSch commented 3 years ago

@maxgrigori Are the selected markers normal "antibody-based" markers or are you using spatial features as well?

maxgrigori commented 3 years ago

Hello Denis,

Thank you very much for answering. I am only selecting antibody-based markers for the analysis.

Best, Max

DenisSch commented 3 years ago

Does this also happen when you run it on one image? Would you be able to share the session or csv so I can check what the issue is?

Best

Denis

maxgrigori commented 3 years ago

Hello Dennis,

It does not happen when I try to run tSNE and PhenoGraph analysis on one image only. But as I do the analysis on all of my images/ROIs (170 small ROIs in total) it occurs.

I'd be very happy to share the session with you! How should I share it? Via mail?

Best, Max

maxgrigori commented 3 years ago

Hello Dennis,

I was unsure how and what to share, as I can not share the MAT-file of the histocat-session here. However, as I would still be very glad for your help, I'll upload the csv-files of two Phenograph-Clusters calculated prior with n=30. One is resulting in the "cross-error" (Cluster 5) mentioned above, the other seems to be able to plot normally (Cluster 20).

I hope this might help. If something else is required, please tell me, as I really can't get behind the underlying issue here.

Very grateful for the help! Best, Max

PG-clusters.zip

DenisSch commented 3 years ago

Dear @maxgrigori

Please drop me a message with your email address to Denis.Schapiro(at)uni-heidelberg.de so we can investigate together during a quick call.

Best

Denis

skylarkfi commented 1 year ago

Hello,

Did you manage to resolve this issue? I'm having similar problems with PhenoGraph clustering. It works fine with 10 images, but when I try with the full set of images (114), some of the clusters get the "cross-chape" and show only white in the heatmap. I'm stuck with this problem and can't get past it. I would appreciate any advice. Thank you!