While running some tests, I had one well that lead to empty ROI tables (because no primary objects where found). When I then wanted to run cellpose within this ROI table, I ran into the following error:
2023-10-10 19:48:49,548; INFO; Now starting loop over 0 ROIs
2023-10-10 19:48:49,548; INFO; End cellpose_segmentation task for /tungstenfs/scratch/gliberal/Users/luetjoel/20230626_deployment_130/fractal-demos/examples/10_2D_to_3D_workflow/output_2D_to_3D_workflow_2/20200812-CardiomyocyteDifferentiation14-Cycle1.zarr/B/03/0, now building pyramids.
2023-10-10 19:48:49,595; INFO; End building pyramids
Traceback (most recent call last):
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib/python3.9/site-packages/fractal_tasks_core/tasks/cellpose_segmentation.py", line 657, in <module>
run_fractal_task(
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/fractal_tasks_core/tasks/_utils.py", line 79, in run_fractal_task
metadata_update = task_function(**pars)
File "pydantic/decorator.py", line 40, in pydantic.decorator.validate_arguments.validate.wrapper_function
from contextlib import _GeneratorContextManager
File "pydantic/decorator.py", line 134, in pydantic.decorator.ValidatedFunction.call
File "pydantic/decorator.py", line 206, in pydantic.decorator.ValidatedFunction.execute
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib/python3.9/site-packages/fractal_tasks_core/tasks/cellpose_segmentation.py", line 619, in cellpose_segmentation
df_well = pd.concat(bbox_dataframe_list, axis=0, ignore_index=True)
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/pandas/util/_decorators.py", line 331, in wrapper
return func(*args, **kwargs)
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/pandas/core/reshape/concat.py", line 368, in concat
op = _Concatenator(
File "/path/to/FRACTAL_TASK_DIR/.fractal/fractal-tasks-core0.12.0/venv/lib64/python3.9/site-packages/pandas/core/reshape/concat.py", line 425, in __init__
raise ValueError("No objects to concatenate")
ValueError: No objects to concatenate
Steps to reproduce:
Workflow to OME-Zarr (e.g. example 01)
Change cellpose parameters so that no objects are found (e.g. put diameter to 1000)
Create output ROI table from cellpose
Then run another Cellpose task using that output ROI table
Goal: No ValueError is created, but the task just creates an empty label image and an empty ROI table.
While running some tests, I had one well that lead to empty ROI tables (because no primary objects where found). When I then wanted to run cellpose within this ROI table, I ran into the following error:
Steps to reproduce:
Goal: No ValueError is created, but the task just creates an empty label image and an empty ROI table.