gating with yaml

[hallucigenia-sparsa]

When trying to use only the SYBR-green stain on command line, the exception below is thrown. In the GUI, the bug can be reproduced on the test files (RI, BT, FP, BH) when specifying the SYBR-Green stain (threshold: 5000). The error msg in the GUI when launching training is: "Error during prediction: Error while processing species file BH: 'dead'"

Command line:

(base) GBW-L-M1030:Validation u0097353$ Traceback (most recent call last):
  File "/opt/anaconda3/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 3805, in get_loc
    return self._engine.get_loc(casted_key)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "index.pyx", line 167, in pandas._libs.index.IndexEngine.get_loc
  File "index.pyx", line 196, in pandas._libs.index.IndexEngine.get_loc
  File "pandas/_libs/hashtable_class_helper.pxi", line 7081, in pandas._libs.hashtable.PyObjectHashTable.get_item
  File "pandas/_libs/hashtable_class_helper.pxi", line 7089, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'dead'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "CellScanner/CellScanner/cellscanner/scripts/apply_umap.py", line 153, in process_files
    process_file(
  File "CellScanner/CellScanner/cellscanner/scripts/apply_umap.py", line 67, in process_file
    df = df[gated_df["dead"] == False]
            ~~~~~~~~^^^^^^^^
  File "/opt/anaconda3/lib/python3.12/site-packages/pandas/core/frame.py", line 4102, in __getitem__
    indexer = self.columns.get_loc(key)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/anaconda3/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 3812, in get_loc
    raise KeyError(key) from err