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[Error] Running seg2explorer #120
Description
Dear segger team,
Hi, all! Hope you been well and thanks for the sharing tool for community:
I am running the most recent segger_dev repo. with Xenium_v2 dataset and have following error when running seg2explorer.
I also saw the other posts (#119, #83) but seem like when running segment function didn't generate cells.zarr.zip but only segger_transcripts.parquet. Any chance I can use this parquet file to visualise segmentation result on Xenium explorer?
Activity
EliHei2 commentedon Jul 28, 2025
please refer to #121
EliHei2 commentedon Jul 31, 2025
@jpark27 could you check the main branch now? the bug should have been fixed now
jpark27 commentedon Aug 1, 2025
Hi, @EliHei2! Thank you so much for updating the scripts.
seg2explorer seems running this time with those codes but come across with following error:
###########################################################
from segger.validation.xenium_explorer import seg2explorer
import dask.dataframe as dd
ddf = dd.read_parquet('/project/simmons_hts/jpark/0_tools/segger_dev/data_segger/RUNTRexBio_SLIDE1/benchmarks/segger_output_0.5_False_4_12_15_3_20250730/segger_transcripts.parquet').compute()
ddf = ddf.dropna()
ddf = ddf[ddf.segger_cell_id != "None"]
ddf = ddf.sort_values("segger_cell_id")
from shapely.geometry import Polygon
seg2explorer(
seg_df=ddf,
source_path=xenium_data_dir,
output_dir="/project/simmons_hts/jpark/0_tools/segger_dev/data_segger/RUNTRexBio_SLIDE1/benchmarks/segger_output_0.5_False_4_12_15_3_20250730",
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,
)
###########################################################
Can you help me how to fix it?
jpark27 commentedon Aug 2, 2025
(Update)
It seem even though
seg2explorerfailed,segger_cell_boundaries.parquetgeneration is working with the corrected scripts. One burning question is, as morphology image and boundary image are having different orientation and scale, is there any function one can easily overlay them?EliHei2 commentedon Sep 5, 2025
@jpark27 the most recent commit should fix all bugs with Xenium explorer, could you please check?
jpark27 commentedon Mar 6, 2026
Hi, @EliHei2! My apologies for such delayed response.
I manage to run Seg2Explorer again and it worked this time and creating following files.
However, when I downloaded "seg_experiment.xenium", "seg_analysis.zarr.zip", "seg_cells.zarr.zip" alongside original ome.tiff image, Xenium explorer throws error like following:
Any chance you have encountered similar issues before?
best wishes,
J