Describe the bug
When "population_cell_mask.csv" is created in the Mantis directory, the unassigned cell ID is not included, which results in a cell population confusingly labelled as "Imported Selection #" after opening up the cell masks in Mantis (see screenshot below). I confirmed that these cells labelled as "Imported Selection #" are actually unassigned cells.
An "unassigned" cell population (cells that had no pixel clusters assigned in them) is correctly assigned to the cell masks and correctly assigned in the cell table, but it is missing in "population_cell_mask.csv", which is generated in plot_utils.create_mantis_dir.
Expected behavior
Add a row to "population_cell_mask.csv" where the unassigned cell ID has the label "unassigned."
To Reproduce
Can delete a few rows from cluster_counts_size_norm before training the SOM and open up the images in Mantis.
Describe the bug When "population_cell_mask.csv" is created in the Mantis directory, the unassigned cell ID is not included, which results in a cell population confusingly labelled as "Imported Selection #" after opening up the cell masks in Mantis (see screenshot below). I confirmed that these cells labelled as "Imported Selection #" are actually unassigned cells.
An "unassigned" cell population (cells that had no pixel clusters assigned in them) is correctly assigned to the cell masks and correctly assigned in the cell table, but it is missing in "population_cell_mask.csv", which is generated in
plot_utils.create_mantis_dir.Expected behavior Add a row to "population_cell_mask.csv" where the unassigned cell ID has the label "unassigned."
To Reproduce Can delete a few rows from
cluster_counts_size_normbefore training the SOM and open up the images in Mantis.