Daniel C. Jones

1. This was a source of confusion beacues `--voxel-layers` sets the initial number of layers, but resolution is increasing while sampling to arrive at 4 times that number. I just...

1. I would do something like this: ```R # You can also read the whole table with `read.csv`, but this is faster if you just need the number of transcripts...

Could you post the contents of the error log it references (`tma2_proseg/XENIUM_RANGER_CS/INSITU_COUNTER_CS/INSITU_COUNTER_CORE/INSITU_ANALYZER/RUN_PCA/fork0/chnk0-u1d2b9fbecf/_errors`)?

Well, that was less useful than I had hoped! You may have to contact 10x support since this doesn't give me much to go on, and they would be better...

It's definitely possible that slightly more transcripts caused in to run out of memory and crash. Usually if it crashes without printing out any kind of error message, an out...

Feel free to ask whatever questions, or open new issues if you run into problems! Brain is very difficult to segment well. I think proseg can do a better job...

In my testing including or excluding negative controls makes very little difference to the quality of segmentation. Including them will use some more memory and take bit longer to run,...