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when I run Cell Segmentation, it reports the following error: no path => skip; no zarr store => skip read. #9
Description
I created a normal workflow, and the original files also exist in the expected directory.
However, when I run Cell Segmentation, it reports the following error in log as shown below:
[Async Register] Allocated log for model=SegmentationNode env=tissuelab-stardist at 20251113_201230
[Custom Node Service] Using existing environment: tissuelab-stardist
bioimageio_utils.py (2): pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
Starting SegmentationNode at port=8001
INFO: Started server process [4964]
INFO: Waiting for application startup.
INFO: Application startup complete.
INFO: Uvicorn running on http://0.0.0.0:8001 (Press CTRL+C to quit)
INFO: 127.0.0.1:61086 - "GET /status HTTP/1.1" 200 OK
[SegmentationNode] /init => inited model/resources (with embedding)
INFO: 127.0.0.1:61089 - "POST /init HTTP/1.1" 200 OK
[SegmentationNode] /read => node_name=SegmentationNode, deps=[], zarr_path=None
[SegmentationNode] no zarr store => skip read.
INFO: 127.0.0.1:57797 - "POST /read HTTP/1.1" 200 OK
[SegmentationNode] create_node success => {'code': 0, 'message': 'Success', 'data': {'message': "Service 'SegmentationNode' already exists in services (idempotent).", 'service_info': {'file': 'K:\\doctor\\tissue_lab\\Src\\Tissuelab-Model-Zoo1111_1833\\Tissuelab-Model-Zoo\\nuclei_segmentation\\StarDist\\segmentation_taskNode.py', 'port': 8001, 'running': False}}}
[SegmentationNode] Serving at port=8001, Press Ctrl+C to exit.
[SegmentationNode] no path => skip.
INFO: 127.0.0.1:57804 - "POST /execute HTTP/1.1" 200 OK
INFO: 127.0.0.1:52670 - "GET /progress HTTP/1.1" 200 OK
[SSE] Progress: 0%
INFO: 127.0.0.1:52672 - "GET /status HTTP/1.1" 200 OK
[SegmentationNode] /init => already done.
INFO: 127.0.0.1:65291 - "POST /init HTTP/1.1" 200 OK
[SegmentationNode] /read => node_name=SegmentationNode, deps=[], zarr_path=None
[SegmentationNode] no zarr store => skip read.
INFO: 127.0.0.1:65294 - "POST /read HTTP/1.1" 200 OK
[SegmentationNode] no path => skip.
INFO: 127.0.0.1:65296 - "POST /execute HTTP/1.1" 200 OK
INFO: 127.0.0.1:57273 - "GET /progress HTTP/1.1" 200 OK
[SSE] Progress: 0%
INFO: 127.0.0.1:57276 - "GET /status HTTP/1.1" 200 OK
[SegmentationNode] /init => already done.
INFO: 127.0.0.1:64759 - "POST /init HTTP/1.1" 200 OK
[SegmentationNode] /read => node_name=SegmentationNode, deps=[], zarr_path=None
[SegmentationNode] no zarr store => skip read.
INFO: 127.0.0.1:64761 - "POST /read HTTP/1.1" 200 OK
[SegmentationNode] no path => skip.
INFO: 127.0.0.1:64765 - "POST /execute HTTP/1.1" 200 OK
How should I correctly specify or configure the input file path for the workflow?
I’d like to make sure that the segmentation node can properly locate the image file.
Environment
OS: Windows 10
TissueLab version: (TissueLab-Setup-1.0.2.exe)
Installation method: (from GitHub / release / other)
Python version: (3.10.6)
Activity
Songhao-LI commentedon Apr 3, 2026
Hi @GreenValue ,
Sorry for the late reply! And thanks for sharing the detailed logs!
From what I can see, the TaskNode you’re using is the zarr-based version, and the key issue is here:
zarr_path=Noneandno path => skip.This is likely due to a version mismatch. The TaskNode you’re using is the zarr-based version, while the platform you’re running expects the H5-based pipeline. As a result, the segmentation node isn’t receiving a valid input path and skips execution.
There are two options to fix this:
This version supports more direct file input and is usually easier to get running locally.
Everything is already set up there, including data handling and model configuration:
https://app.tissuelab.org/
We’re actively improving the offline experience to make this smoother and reduce this kind of configuration overhead. Let me know if you run into any issues.