Cell label missing in heatmap in lineage tracing in MGX


I have been using MGX for lineage tracing for a while now, but very occasionally, there will be some cells having their labels removed for some reason when I try to display samples in heatmaps. So here’s what I mean labels missing:

I have a sample that’s taken at two time points and I have labeled the parents on time point 2 (right) based on time point 1(left). The cells circled in white will be cells that have problems later, but you can see at this step, they are correctly labeled.

Then I did Check Correpondance and corrected all the errors. Those cells didn’t appear to have any error at this step either:

However, if I use the heatmap to display the increase/decrease in growth or compute/display PDG, the labels of cells are gone:

I have tried to label the parents again or re-seed/segment in the original meshes for both time points, but nothing seemed to work. Do you know why this happens? Also it definitely doesn’t show up in all the samples, but this is about the third time (i.e. on three different samples that were processed this month and the last months). Very confused!

Any help to solve this problem is really appreciated!!


Can you put this mesh somewhere so that I can have a look?

Yes! I put them in this google drive folder: https://drive.google.com/drive/folders/1N9uigBVBKrurRXamozKamdoMxg5DPtOW?usp=sharing

The 20201102_B4 is for time point 1, 20201105_B4 is for time point 2, and the csv file is for parental labeling.

Please let me know if you have any problems accessing the folder or need more materials.


Please make sure the “Force Recalculation” box is checked on the heat map dialog. We should probably make that the default.