I am trying to run ProSeg v3.0.12 using a SpatialData zarr input that contains:
- transcript coordinates as points
- cell boundary geometries as shapes
- intended use of prior cell segmentation via --zarr-shape
However, ProSeg fails during input parsing and does not correctly handle this SpatialData structure, even though it follows the SpatialData specification.
[Environment]
- ProSeg version: 3.0.12
- Installation: cargo install proseg
- OS: Linux (HPC cluster)
- SpatialData generated with: spatialdata (Python)
[SpatialData input structure]
The input zarr has the following structure:
xenium_proseg_input.zarr
├── points/
│ └── transcripts/
│ └── points.parquet
├── shapes/
│ └── cell_boundaries/
├── zmetadata
Details:
- points/transcripts contains transcript-level coordinates (x, y)
- shapes/cell_boundaries contains polygon geometries for cells
- The shapes are intended to be used as prior segmentation
Command used
proseg
--zarr xenium_proseg_input.zarr
--zarr-shape xenium_proseg_input.zarr
--zarr-shape-geometry-column geometry
--zarr-shape-cell-id-column cell_id
--use-cell-initialization
--prior-seg-reassignment-prob 0.3
ProSeg terminates with the following error:
Missing required argument: --x
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace
This occurs even though transcript coordinates are present in points/transcripts and no table-based or CSV-based input is being used.
I am trying to run ProSeg v3.0.12 using a SpatialData zarr input that contains:
However, ProSeg fails during input parsing and does not correctly handle this SpatialData structure, even though it follows the SpatialData specification.
[Environment]
[SpatialData input structure]
The input zarr has the following structure:
xenium_proseg_input.zarr
├── points/
│ └── transcripts/
│ └── points.parquet
├── shapes/
│ └── cell_boundaries/
├── zmetadata
Details:
Command used
proseg
--zarr xenium_proseg_input.zarr
--zarr-shape xenium_proseg_input.zarr
--zarr-shape-geometry-column geometry
--zarr-shape-cell-id-column cell_id
--use-cell-initialization
--prior-seg-reassignment-prob 0.3
ProSeg terminates with the following error:
Missing required argument: --x
note: run with
RUST_BACKTRACE=1environment variable to display a backtraceThis occurs even though transcript coordinates are present in points/transcripts and no table-based or CSV-based input is being used.