angelolab / angelolab/ark-analysis
"Unassigned" label not included in "population_cell_mask.csv" for Mantis
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Descrizione
**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.

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