Error during PhenoGraph calculation

[maxgrigori]

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...

[DenisSch]

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

[maxgrigori]

Hello Denis,

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

Best, Max

[DenisSch]

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]

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]

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]

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]

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!