[release/v2-stable] Seg2Explorer not working

[jpark27]

Dear @EliHei2

Hi, Elias! Hope you been well.
Related to discussion we had on segger v1 (EliHei2/segger_dev#134), I successfully run "v2-stable" on my small dataset and run Seg2Explorer as follows:

#############################################################
xenium_data_dir = "/project/simmons_hts/shared/04_12_2023_xenium_trial_1/S2"

from segger.validation.xenium_explorer import seg2explorer
import dask.dataframe as dd
from shapely.geometry import Polygon

ddf = dd.read_parquet('/project/IBD_CD4/jpark/0_tools/segger/IBD_CD4/04_12_2023_xenium_trial_1/S2/transcripts_segmented.parquet').compute()
ddf = ddf.dropna()
ddf = ddf[ddf.segger_cell_id != "None"]
ddf = ddf.sort_values("segger_cell_id")

ddf = ddf.rename(columns={
'x': 'x_location',
'y': 'y_location',
'z': 'z_location'
})
ddf['overlaps_nucleus'] = 0 # no nucleus info available, set to 0

seg2explorer(
seg_df=ddf,
source_path=xenium_data_dir,
output_dir="/project/IBD_CD4/jpark/0_tools/segger/IBD_CD4/04_12_2023_xenium_trial_1/S2/",
cells_filename="seg_cells",
analysis_filename="seg_analysis",
xenium_filename="seg_experiment.xenium",
analysis_df=None,
cell_id_columns="segger_cell_id",
area_low=10,
area_high=100,
)
#############################################################

But even with these new outputs from v2, I still can't open segmentation result on Xenium explorer (v4.1.1). Any piece of advice on this?

[EliHei2]

hey! this is a zarr2 vs zarr3 issue I'm trying to fix, will get back to you asap on this. in the meanwhile please use v2-incremental branch which is a debuged version of the v2-stable branch.