CellProfiler plugins (RunCellpose and Runilastik) working only in test mode and not in analysis mode using Docker Desktop in Windows computer

This issue was mentioned in the forum ([1](https://forum.image.sc/t/modules-running-through-docker-desktop-as-plugins-in-cellprofiler-suddenly-stopped-working-in-analysis-mode/117959),[2](https://forum.image.sc/t/cellprofiler-works-in-test-mode-but-not-to-analyze-images/118448/9)) and was briefly discussed on [Slack](https://broadinstitute.slack.com/archives/G01CRK68RNW/p1766007374976689) as well.

In short, the pipelines with `RunCellpose` runs fine in test mode, but in analysis mode, containers do not seem to appear. After waiting for a while, when the run is cancelled, `RunCellpose` logs start appearing but the run then cancels.

I was able to replicate the issue in my personal Windows computer and have added the notes below:

**CellProfiler v4.2.8**
**Docker Desktop v4.55.0**
**Podman DEsktop v1.24.2**
**RunCellpose v2**
**Image cellprofiler/runcellpose_with_pretrained**
       Tag 2.3.2
       ImageID sha256:7bdb0f83ac9053ee5dccc324d3176dd56f076c38ab18ddf0e48b614238f7215a
**Windows Home 25H2**


### Running beginner segmentation bonus exercise pipeline with order of the modules slightly changed and an extra `OverlayOutlines` added

1. Test mode (Docker Desktop)

```
Starting CellProfiler 4.2.8
Could not load runimagejscript
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
    import cpij.bridge as ijbridge, cpij.server as ijserver
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
    import atexit, cpij.server as ijserver
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
    import jpype, imagej, multiprocessing, socket, threading, time
ModuleNotFoundError: No module named 'jpype'
Could not load runomnipose
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
    from cellpose_omni import models, io, core, plot
ModuleNotFoundError: No module named 'cellpose_omni'
Could not load runstardist
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
    from stardist.models import StarDist2D, StarDist3D
ModuleNotFoundError: No module named 'stardist'
could not load these modules: runimagejscript,runomnipose,runstardist
C:\Users\shata\CellProfiler-plugins\active_plugins\runcellpose.py:968: UserWarning: c:\users\shata\.cellprofiler_temp\a30345b8-5359-42aa-b667-7ab850346a89\img\a30345b8-5359-42aa-b667-7ab850346a89.tiff is a low contrast image
  skimage.io.imsave(temp_img_path, x_data)
['docker', 'run', '--rm', '-v', 'c:\\users\\shata\\.cellprofiler_temp\\a30345b8-5359-42aa-b667-7ab850346a89:/data', 'cellprofiler/runcellpose_with_pretrained:2.3.2', 'cellpose', '--verbose', '--dir', '/data/img', '--pretrained_model', 'nuclei', '--chan', '0', '--chan2', '0', '--diameter', '30', '--cellprob_threshold', '0.0', '--min_size', '15', '--anisotropy', '0.0', '--flow_threshold', '0.4', '--stitch_threshold', '0.0', '--exclude_on_edges']
creating new log file
2025-12-19 18:35:33,579 [INFO] WRITING LOG OUTPUT TO /root/.cellpose/run.log
2025-12-19 18:35:33,579 [INFO]
cellpose version:       2.3.2
platform:               linux
python version:         3.9.12
torch version:          1.13.0
2025-12-19 18:35:33,579 [INFO] >>>> using CPU
2025-12-19 18:35:33,609 [INFO] >>>> running cellpose on 1 images using chan_to_seg GRAY and chan (opt) NONE
2025-12-19 18:35:33,609 [INFO] >>>> using CPU
2025-12-19 18:35:33,609 [INFO] >> nuclei << model set to be used
2025-12-19 18:35:33,830 [INFO] >>>> model diam_mean =  17.000 (ROIs rescaled to this size during training)
2025-12-19 18:35:33,830 [INFO] >>>> using diameter 30.000 for all images
2025-12-19 18:35:33,834 [INFO] 0%|          | 0/1 [00:00<?, ?it/s]
2025-12-19 18:35:33,853 [INFO] ~~~ FINDING MASKS ~~~
2025-12-19 18:35:42,564 [INFO] >>>> TOTAL TIME 8.71 sec
2025-12-19 18:35:43,114 [INFO] 100%|##########| 1/1 [00:09<00:00,  9.28s/it]
2025-12-19 18:35:43,114 [INFO] 100%|##########| 1/1 [00:09<00:00,  9.28s/it]
2025-12-19 18:35:43,114 [INFO] >>>> completed in 9.535 sec
```
Container appeared
<img width="967" height="279" alt="image" src="https://github.com/user-attachments/assets/5f3e4753-de03-4d96-99dd-67ba6f27c682" />


2. Analysis mode (Docker Desktop)

```
Progress Counter({'Unprocessed': 10})
Starting workers on address tcp://127.0.0.1:51706
Worker 0:
          Starting job
Progress Counter({'Unprocessed': 9, 'InProcess': 1})
Worker 0: Could not load runimagejscript
Worker 0: Traceback (most recent call last):
Worker 0:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
Worker 0:     import cpij.bridge as ijbridge, cpij.server as ijserver
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
Worker 0:     import atexit, cpij.server as ijserver
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
Worker 0:     import jpype, imagej, multiprocessing, socket, threading, time
Worker 0: ModuleNotFoundError: No module named 'jpype'
Worker 0: Could not load runomnipose
Worker 0: Traceback (most recent call last):
Worker 0:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
Worker 0:     from cellpose_omni import models, io, core, plot
Worker 0: ModuleNotFoundError: No module named 'cellpose_omni'
Worker 0: Could not load runstardist
Worker 0: Traceback (most recent call last):
Worker 0:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
Worker 0:     from stardist.models import StarDist2D, StarDist3D
Worker 0: ModuleNotFoundError: No module named 'stardist'
Worker 0: could not load these modules: runimagejscript,runomnipose,runstardist
Worker 0: Doing job: 1
Worker 0: Fri Dec 19 13:37:11 2025: Image # 1, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 13:37:11 2025: Image # 1, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 13:37:11 2025: Image # 1, module NamesAndTypes # 3: CPU_time = 1.25 secs, Wall_time = 1.29 secs
Worker 0: Fri Dec 19 13:37:12 2025: Image # 1, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 13:37:12 2025: Image # 1, module RescaleIntensity # 5: CPU_time = 0.06 secs, Wall_time = 0.05 secs
Worker 0: Fri Dec 19 13:37:12 2025: Image # 1, module IdentifyPrimaryObjects # 6: CPU_time = 0.28 secs, Wall_time = 0.28 secs
Worker 0: Fri Dec 19 13:37:13 2025: Image # 1, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
```
No containers appear
<img width="1344" height="536" alt="image" src="https://github.com/user-attachments/assets/101680f2-395b-4bbe-a96b-946cca89b2bb" />

This appears the moment I hit `Stop Analysis`

```
Worker 1:
          Starting CellProfiler 4.2.8
Worker 2:
          Starting CellProfiler 4.2.8
Worker 1: Cancelling worker
Worker 2: Cancelling worker
Worker 0: creating new log file
Worker 0: 2025-12-19 18:41:13,079 [INFO] WRITING LOG OUTPUT TO /root/.cellpose/run.log
Worker 0: 2025-12-19 18:41:13,079 [INFO]
Worker 0: cellpose version:     2.3.2
Worker 0: platform:             linux
Worker 0: python version:       3.9.12
Worker 0: torch version:        1.13.0
Worker 0: 2025-12-19 18:41:13,079 [INFO] >>>> using CPU
Worker 0: 2025-12-19 18:41:13,106 [INFO] >>>> running cellpose on 1 images using chan_to_seg GRAY and chan (opt) NONE
Worker 0: 2025-12-19 18:41:13,106 [INFO] >>>> using CPU
Worker 0: 2025-12-19 18:41:13,107 [INFO] >> nuclei << model set to be used
Worker 0: 2025-12-19 18:41:13,312 [INFO] >>>> model diam_mean =  17.000 (ROIs rescaled to this size during training)
Worker 0: 2025-12-19 18:41:13,313 [INFO] >>>> using diameter 30.000 for all images
Worker 0: 2025-12-19 18:41:13,317 [INFO] 0%|          | 0/1 [00:00<?, ?it/s]
Worker 0: 2025-12-19 18:41:13,337 [INFO] ~~~ FINDING MASKS ~~~
Cancelled!
Worker 0: 2025-12-19 18:41:21,775 [INFO] >>>> TOTAL TIME 8.44 sec
Worker 0: 2025-12-19 18:41:21,909 [INFO] 100%|##########| 1/1 [00:08<00:00,  8.59s/it]
Worker 0: 2025-12-19 18:41:21,909 [INFO] 100%|##########| 1/1 [00:08<00:00,  8.59s/it]
Worker 0: 2025-12-19 18:41:21,909 [INFO] >>>> completed in 8.830 sec
```

3. Analysis mode without `RunCellpose` (completes fine)

```
Starting CellProfiler 4.2.8
Could not load runimagejscript
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
    import cpij.bridge as ijbridge, cpij.server as ijserver
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
    import atexit, cpij.server as ijserver
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
    import jpype, imagej, multiprocessing, socket, threading, time
ModuleNotFoundError: No module named 'jpype'
Could not load runomnipose
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
    from cellpose_omni import models, io, core, plot
ModuleNotFoundError: No module named 'cellpose_omni'
Could not load runstardist
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
    from stardist.models import StarDist2D, StarDist3D
ModuleNotFoundError: No module named 'stardist'
could not load these modules: runimagejscript,runomnipose,runstardist
Progress Counter({'Unprocessed': 10})
Starting workers on address tcp://127.0.0.1:62023
Worker 0:
          Starting job
Progress Counter({'Unprocessed': 9, 'InProcess': 1})
Worker 0: Could not load runimagejscript
Worker 0: Traceback (most recent call last):
Worker 0:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
Worker 0:     import cpij.bridge as ijbridge, cpij.server as ijserver
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
Worker 0:     import atexit, cpij.server as ijserver
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
Worker 0:     import jpype, imagej, multiprocessing, socket, threading, time
Worker 0: ModuleNotFoundError: No module named 'jpype'
Worker 0: Could not load runomnipose
Worker 0: Traceback (most recent call last):
Worker 0:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
Worker 0:     from cellpose_omni import models, io, core, plot
Worker 0: ModuleNotFoundError: No module named 'cellpose_omni'
Worker 0: Could not load runstardist
Worker 0: Traceback (most recent call last):
Worker 0:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 0:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
Worker 0:     from stardist.models import StarDist2D, StarDist3D
Worker 0: ModuleNotFoundError: No module named 'stardist'
Worker 0: could not load these modules: runimagejscript,runomnipose,runstardist
Worker 0: Doing job: 1
Worker 0: Fri Dec 19 14:04:31 2025: Image # 1, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:31 2025: Image # 1, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:31 2025: Image # 1, module NamesAndTypes # 3: CPU_time = 1.22 secs, Wall_time = 1.33 secs
Worker 0: Fri Dec 19 14:04:32 2025: Image # 1, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:32 2025: Image # 1, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 0: Fri Dec 19 14:04:32 2025: Image # 1, module IdentifyPrimaryObjects # 6: CPU_time = 0.30 secs, Wall_time = 0.29 secs
Worker 0: Fri Dec 19 14:04:32 2025: Image # 1, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 0: Fri Dec 19 14:04:32 2025: Image # 1, module SaveImages # 10: CPU_time = 0.08 secs, Wall_time = 0.08 secs
Progress Counter({'Unprocessed': 9, 'FinishedWaitingMeasurements': 1})
Worker 1:
          Starting job
Worker 2:
          Starting job
Progress Counter({'Unprocessed': 7, 'InProcess': 2, 'Done': 1})
Worker 2: Could not load runimagejscript
Worker 2: Traceback (most recent call last):
Worker 2:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 2:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
Worker 2:     import cpij.bridge as ijbridge, cpij.server as ijserver
Worker 2:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
Worker 2:     import atexit, cpij.server as ijserver
Worker 2:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
Worker 2:     import jpype, imagej, multiprocessing, socket, threading, time
Worker 2: ModuleNotFoundError: No module named 'jpype'
Worker 2: Could not load runomnipose
Worker 2: Traceback (most recent call last):
Worker 2:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 2:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
Worker 2:     from cellpose_omni import models, io, core, plot
Worker 2: ModuleNotFoundError: No module named 'cellpose_omni'
Worker 1: Could not load runimagejscript
Worker 1: Traceback (most recent call last):
Worker 1:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
Worker 1:     import cpij.bridge as ijbridge, cpij.server as ijserver
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
Worker 1:     import atexit, cpij.server as ijserver
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
Worker 1:     import jpype, imagej, multiprocessing, socket, threading, time
Worker 1: ModuleNotFoundError: No module named 'jpype'
Worker 2: Could not load runstardist
Worker 2: Traceback (most recent call last):
Worker 2:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 2:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
Worker 2:     from stardist.models import StarDist2D, StarDist3D
Worker 2: ModuleNotFoundError: No module named 'stardist'
Worker 1: Could not load runomnipose
Worker 1: Traceback (most recent call last):
Worker 1:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
Worker 1:     from cellpose_omni import models, io, core, plot
Worker 1: ModuleNotFoundError: No module named 'cellpose_omni'
Worker 1: Could not load runstardist
Worker 1: Traceback (most recent call last):
Worker 1:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
Worker 1:     from stardist.models import StarDist2D, StarDist3D
Worker 1: ModuleNotFoundError: No module named 'stardist'
Worker 2: could not load these modules: runimagejscript,runomnipose,runstardist
Worker 1: could not load these modules: runimagejscript,runomnipose,runstardist
Worker 0: Starting job
Progress Counter({'Unprocessed': 6, 'InProcess': 3, 'Done': 1})
Worker 0: Doing job: 4
Worker 2: Doing job: 3
Worker 1: Doing job: 2
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:38 2025: Image # 3, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:38 2025: Image # 2, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:38 2025: Image # 3, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:38 2025: Image # 2, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module NamesAndTypes # 3: CPU_time = 0.47 secs, Wall_time = 0.45 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.06 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module IdentifyPrimaryObjects # 6: CPU_time = 0.25 secs, Wall_time = 0.27 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module OverlayOutlines # 7: CPU_time = 0.03 secs, Wall_time = 0.02 secs
Worker 0: Fri Dec 19 14:04:38 2025: Image # 4, module SaveImages # 10: CPU_time = 0.06 secs, Wall_time = 0.08 secs
Progress Counter({'Unprocessed': 6, 'InProcess': 2, 'Done': 1, 'FinishedWaitingMeasurements': 1})
Worker 1: Fri Dec 19 14:04:38 2025: Image # 2, module NamesAndTypes # 3: CPU_time = 1.25 secs, Wall_time = 1.43 secs
Worker 1: Fri Dec 19 14:04:39 2025: Image # 2, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:38 2025: Image # 3, module NamesAndTypes # 3: CPU_time = 1.17 secs, Wall_time = 1.45 secs
Worker 2: Fri Dec 19 14:04:39 2025: Image # 3, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:39 2025: Image # 2, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 2: Fri Dec 19 14:04:39 2025: Image # 3, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 2: Fri Dec 19 14:04:39 2025: Image # 3, module IdentifyPrimaryObjects # 6: CPU_time = 0.30 secs, Wall_time = 0.31 secs
Worker 1: Fri Dec 19 14:04:39 2025: Image # 2, module IdentifyPrimaryObjects # 6: CPU_time = 0.31 secs, Wall_time = 0.32 secs
Worker 2: Fri Dec 19 14:04:39 2025: Image # 3, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 1: Fri Dec 19 14:04:39 2025: Image # 2, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 1: Fri Dec 19 14:04:39 2025: Image # 2, module SaveImages # 10: CPU_time = 0.08 secs, Wall_time = 0.09 secs
Worker 2: Fri Dec 19 14:04:39 2025: Image # 3, module SaveImages # 10: CPU_time = 0.09 secs, Wall_time = 0.10 secs
Progress Counter({'Unprocessed': 6, 'Done': 2, 'FinishedWaitingMeasurements': 1, 'InProcess': 1})
Worker 0: Starting job
Progress Counter({'Unprocessed': 6, 'Done': 2, 'FinishedWaitingMeasurements': 2})
Worker 0: Doing job: 5
Progress Counter({'Unprocessed': 5, 'Done': 3, 'FinishedWaitingMeasurements': 1, 'InProcess': 1})
Worker 1: Starting job
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Doing job: 6
Progress Counter({'Done': 4, 'Unprocessed': 4, 'InProcess': 2})
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module NamesAndTypes # 3: CPU_time = 0.39 secs, Wall_time = 0.40 secs
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module IdentifyPrimaryObjects # 6: CPU_time = 0.27 secs, Wall_time = 0.26 secs
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 0: Fri Dec 19 14:04:42 2025: Image # 5, module SaveImages # 10: CPU_time = 0.08 secs, Wall_time = 0.08 secs
Worker 2: Starting job
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Progress Counter({'Done': 4, 'Unprocessed': 3, 'InProcess': 2, 'FinishedWaitingMeasurements': 1})
Worker 2: Doing job: 7
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module NamesAndTypes # 3: CPU_time = 0.47 secs, Wall_time = 0.44 secs
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module IdentifyPrimaryObjects # 6: CPU_time = 0.27 secs, Wall_time = 0.26 secs
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 1: Fri Dec 19 14:04:43 2025: Image # 6, module SaveImages # 10: CPU_time = 0.06 secs, Wall_time = 0.07 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Progress Counter({'Done': 5, 'Unprocessed': 3, 'FinishedWaitingMeasurements': 1, 'InProcess': 1})
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module NamesAndTypes # 3: CPU_time = 0.44 secs, Wall_time = 0.45 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module RescaleIntensity # 5: CPU_time = 0.06 secs, Wall_time = 0.05 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module IdentifyPrimaryObjects # 6: CPU_time = 0.27 secs, Wall_time = 0.27 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 2: Fri Dec 19 14:04:44 2025: Image # 7, module SaveImages # 10: CPU_time = 0.06 secs, Wall_time = 0.06 secs
Worker 0: Starting job
Worker 0: Doing job: 8
Progress Counter({'Done': 6, 'Unprocessed': 2, 'FinishedWaitingMeasurements': 1, 'InProcess': 1})
Worker 1: Starting job
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Doing job: 9
Progress Counter({'Done': 7, 'InProcess': 2, 'Unprocessed': 1})
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module NamesAndTypes # 3: CPU_time = 0.39 secs, Wall_time = 0.41 secs
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module IdentifyPrimaryObjects # 6: CPU_time = 0.25 secs, Wall_time = 0.27 secs
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 0: Fri Dec 19 14:04:46 2025: Image # 8, module SaveImages # 10: CPU_time = 0.08 secs, Wall_time = 0.09 secs
Worker 2: Starting job
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Progress Counter({'Done': 7, 'InProcess': 2, 'FinishedWaitingMeasurements': 1})
Worker 2: Doing job: 10
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module NamesAndTypes # 3: CPU_time = 0.42 secs, Wall_time = 0.37 secs
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module RescaleIntensity # 5: CPU_time = 0.06 secs, Wall_time = 0.05 secs
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module IdentifyPrimaryObjects # 6: CPU_time = 0.28 secs, Wall_time = 0.28 secs
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module OverlayOutlines # 7: CPU_time = 0.02 secs, Wall_time = 0.02 secs
Worker 1: Fri Dec 19 14:04:47 2025: Image # 9, module SaveImages # 10: CPU_time = 0.06 secs, Wall_time = 0.07 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Progress Counter({'Done': 8, 'FinishedWaitingMeasurements': 1, 'InProcess': 1})
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module NamesAndTypes # 3: CPU_time = 0.41 secs, Wall_time = 0.39 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module RescaleIntensity # 5: CPU_time = 0.05 secs, Wall_time = 0.05 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module IdentifyPrimaryObjects # 6: CPU_time = 0.27 secs, Wall_time = 0.30 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module OverlayOutlines # 7: CPU_time = 0.00 secs, Wall_time = 0.02 secs
Worker 2: Fri Dec 19 14:04:48 2025: Image # 10, module SaveImages # 10: CPU_time = 0.08 secs, Wall_time = 0.07 secs
Progress Counter({'Done': 9, 'FinishedWaitingMeasurements': 1})
Progress Counter({'Done': 10})
Finished!
Worker 0: Starting CellProfiler 4.2.8
Worker 2: Starting CellProfiler 4.2.8
Worker 0: Running module Images 1
Worker 2: Running module Images 1
Worker 0: Running module Metadata 2
Worker 2: Running module Metadata 2
Worker 0: Running module NamesAndTypes 3
Worker 2: Running module NamesAndTypes 3
Worker 0: Running module Groups 4
Worker 2: Running module Groups 4
Worker 0: Running module RescaleIntensity 5
Worker 2: Running module RescaleIntensity 5
Worker 0: Running module IdentifyPrimaryObjects 6
Worker 2: Running module IdentifyPrimaryObjects 6
Worker 0: Running module OverlayOutlines 7
Worker 2: Running module OverlayOutlines 7
Worker 0: Running module SaveImages 10
Worker 2: Running module SaveImages 10
Worker 0: Running module Images 1
Worker 2: Running module Images 1
Worker 0: Running module Metadata 2
Worker 0: Running module NamesAndTypes 3
Worker 2: Running module Metadata 2
Worker 0: Running module Groups 4
Worker 2: Running module NamesAndTypes 3
Worker 0: Running module RescaleIntensity 5
Worker 2: Running module Groups 4
Worker 0: Running module IdentifyPrimaryObjects 6
Worker 2: Running module RescaleIntensity 5
Worker 0: Running module OverlayOutlines 7
Worker 2: Running module IdentifyPrimaryObjects 6
Worker 0: Running module SaveImages 10
Worker 2: Running module OverlayOutlines 7
Worker 0: Running module Images 1
Worker 2: Running module SaveImages 10
Worker 0: Running module Metadata 2
Worker 2: Running module Images 1
Worker 0: Running module NamesAndTypes 3
Worker 2: Running module Metadata 2
Worker 0: Running module Groups 4
Worker 2: Running module NamesAndTypes 3
Worker 0: Running module RescaleIntensity 5
Worker 2: Running module Groups 4
Worker 0: Running module IdentifyPrimaryObjects 6
Worker 2: Running module RescaleIntensity 5
Worker 0: Running module OverlayOutlines 7
Worker 2: Running module IdentifyPrimaryObjects 6
Worker 0: Running module SaveImages 10
Worker 2: Running module OverlayOutlines 7
Worker 0: Running module Images 1
Worker 2: Running module SaveImages 10
Worker 0: Running module Metadata 2
Worker 2: Cancelling worker
Worker 0: Running module NamesAndTypes 3
Worker 0: Running module Groups 4
Worker 0: Running module RescaleIntensity 5
Worker 0: Running module IdentifyPrimaryObjects 6
Worker 0: Running module OverlayOutlines 7
Worker 0: Running module SaveImages 10
Worker 0: Cancelling worker
Worker 1: Starting CellProfiler 4.2.8
Worker 1: Running module Images 1
Worker 1: Running module Metadata 2
Worker 1: Running module NamesAndTypes 3
Worker 1: Running module Groups 4
Worker 1: Running module RescaleIntensity 5
Worker 1: Running module IdentifyPrimaryObjects 6
Worker 1: Running module OverlayOutlines 7
Worker 1: Running module SaveImages 10
Worker 1: Running module Images 1
Worker 1: Running module Metadata 2
Worker 1: Running module NamesAndTypes 3
Worker 1: Running module Groups 4
Worker 1: Running module RescaleIntensity 5
Worker 1: Running module IdentifyPrimaryObjects 6
Worker 1: Running module OverlayOutlines 7
Worker 1: Running module SaveImages 10
Worker 1: Running module Images 1
Worker 1: Running module Metadata 2
Worker 1: Running module NamesAndTypes 3
Worker 1: Running module Groups 4
Worker 1: Running module RescaleIntensity 5
Worker 1: Running module IdentifyPrimaryObjects 6
Worker 1: Running module OverlayOutlines 7
Worker 1: Running module SaveImages 10
Worker 1: Cancelling worker
```

3. Test mode (Podman)

```
Starting CellProfiler 4.2.8
Could not load runimagejscript
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
    import cpij.bridge as ijbridge, cpij.server as ijserver
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
    import atexit, cpij.server as ijserver
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
    import jpype, imagej, multiprocessing, socket, threading, time
ModuleNotFoundError: No module named 'jpype'
Could not load runomnipose
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
    from cellpose_omni import models, io, core, plot
ModuleNotFoundError: No module named 'cellpose_omni'
Could not load runstardist
Traceback (most recent call last):
  File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
  File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
    from stardist.models import StarDist2D, StarDist3D
ModuleNotFoundError: No module named 'stardist'
could not load these modules: runimagejscript,runomnipose,runstardist
C:\Users\shata\CellProfiler-plugins\active_plugins\runcellpose.py:968: UserWarning: c:\users\shata\.cellprofiler_temp\d4f2a162-3d01-4a76-ab5f-50706615ae0c\img\d4f2a162-3d01-4a76-ab5f-50706615ae0c.tiff is a low contrast image
  skimage.io.imsave(temp_img_path, x_data)
['podman', 'run', '--rm', '-v', 'c:\\users\\shata\\.cellprofiler_temp\\d4f2a162-3d01-4a76-ab5f-50706615ae0c:/data', 'cellprofiler/runcellpose_with_pretrained:2.3.2', 'cellpose', '--verbose', '--dir', '/data/img', '--pretrained_model', 'nuclei', '--chan', '0', '--chan2', '0', '--diameter', '30', '--cellprob_threshold', '0.0', '--min_size', '15', '--anisotropy', '0.0', '--flow_threshold', '0.4', '--stitch_threshold', '0.0', '--exclude_on_edges']
creating new log file
2025-12-19 21:13:10,187 [INFO] WRITING LOG OUTPUT TO /root/.cellpose/run.log
2025-12-19 21:13:10,187 [INFO]
cellpose version:       2.3.2
platform:               linux
python version:         3.9.12
torch version:          1.13.0
2025-12-19 21:13:10,187 [INFO] >>>> using CPU
2025-12-19 21:13:10,212 [INFO] >>>> running cellpose on 1 images using chan_to_seg GRAY and chan (opt) NONE
2025-12-19 21:13:10,212 [INFO] >>>> using CPU
2025-12-19 21:13:10,212 [INFO] >> nuclei << model set to be used
2025-12-19 21:13:10,404 [INFO] >>>> model diam_mean =  17.000 (ROIs rescaled to this size during training)
2025-12-19 21:13:10,405 [INFO] >>>> using diameter 30.000 for all images
2025-12-19 21:13:10,406 [INFO] 0%|          | 0/1 [00:00<?, ?it/s]
2025-12-19 21:13:10,424 [INFO] ~~~ FINDING MASKS ~~~
2025-12-19 21:13:19,849 [INFO] >>>> TOTAL TIME 9.43 sec
2025-12-19 21:13:19,971 [INFO] 100%|##########| 1/1 [00:09<00:00,  9.56s/it]
2025-12-19 21:13:19,972 [INFO] 100%|##########| 1/1 [00:09<00:00,  9.57s/it]
2025-12-19 21:13:19,972 [INFO] >>>> completed in 9.785 sec

```
Container appears

<img width="1044" height="202" alt="image" src="https://github.com/user-attachments/assets/10d26fea-1ce5-44f4-8806-159a7bd4b29a" />

4. Analysis mode (Podman)

```
Progress Counter({'Unprocessed': 10})
Starting workers on address tcp://127.0.0.1:62653
Worker 1:
          Starting job
Progress Counter({'Unprocessed': 9, 'InProcess': 1})
Worker 1: Could not load runimagejscript
Worker 1: Traceback (most recent call last):
Worker 1:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runimagejscript.py", line 15, in <module>
Worker 1:     import cpij.bridge as ijbridge, cpij.server as ijserver
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\bridge.py", line 3, in <module>
Worker 1:     import atexit, cpij.server as ijserver
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\cpij\server.py", line 15, in <module>
Worker 1:     import jpype, imagej, multiprocessing, socket, threading, time
Worker 1: ModuleNotFoundError: No module named 'jpype'
Worker 1: Could not load runomnipose
Worker 1: Traceback (most recent call last):
Worker 1:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runomnipose.py", line 9, in <module>
Worker 1:     from cellpose_omni import models, io, core, plot
Worker 1: ModuleNotFoundError: No module named 'cellpose_omni'
Worker 1: Could not load runstardist
Worker 1: Traceback (most recent call last):
Worker 1:   File "cellprofiler_core\utilities\core\modules\__init__.py", line 71, in add_module
Worker 1:   File "C:\Users\shata\CellProfiler-plugins\active_plugins\runstardist.py", line 9, in <module>
Worker 1:     from stardist.models import StarDist2D, StarDist3D
Worker 1: ModuleNotFoundError: No module named 'stardist'
Worker 1: could not load these modules: runimagejscript,runomnipose,runstardist
Worker 1: Doing job: 1
Worker 1: Fri Dec 19 16:15:02 2025: Image # 1, module Images # 1: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 16:15:02 2025: Image # 1, module Metadata # 2: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 16:15:02 2025: Image # 1, module NamesAndTypes # 3: CPU_time = 1.11 secs, Wall_time = 1.23 secs
Worker 1: Fri Dec 19 16:15:03 2025: Image # 1, module Groups # 4: CPU_time = 0.00 secs, Wall_time = 0.00 secs
Worker 1: Fri Dec 19 16:15:03 2025: Image # 1, module RescaleIntensity # 5: CPU_time = 0.06 secs, Wall_time = 0.05 secs
Worker 1: Fri Dec 19 16:15:03 2025: Image # 1, module IdentifyPrimaryObjects # 6: CPU_time = 0.27 secs, Wall_time = 0.27 secs
Worker 0:
          Starting CellProfiler 4.2.8
Worker 2:
          Starting CellProfiler 4.2.8
Worker 0: Cancelling worker
Worker 2: Cancelling worker
Worker 1: creating new log file
Worker 1: 2025-12-19 21:16:32,076 [INFO] WRITING LOG OUTPUT TO /root/.cellpose/run.log
Worker 1: 2025-12-19 21:16:32,077 [INFO]
Worker 1: cellpose version:     2.3.2
Worker 1: platform:             linux
Worker 1: python version:       3.9.12
Worker 1: torch version:        1.13.0
Worker 1: 2025-12-19 21:16:32,077 [INFO] >>>> using CPU
Worker 1: 2025-12-19 21:16:32,113 [INFO] >>>> running cellpose on 1 images using chan_to_seg GRAY and chan (opt) NONE
Worker 1: 2025-12-19 21:16:32,113 [INFO] >>>> using CPU
Worker 1: 2025-12-19 21:16:32,114 [INFO] >> nuclei << model set to be used
Worker 1: 2025-12-19 21:16:32,333 [INFO] >>>> model diam_mean =  17.000 (ROIs rescaled to this size during training)
Worker 1: 2025-12-19 21:16:32,333 [INFO] >>>> using diameter 30.000 for all images
Worker 1: 2025-12-19 21:16:32,336 [INFO] 0%|          | 0/1 [00:00<?, ?it/s]
Worker 1: 2025-12-19 21:16:32,356 [INFO] ~~~ FINDING MASKS ~~~
Cancelled!
Worker 1: 2025-12-19 21:16:44,830 [INFO] >>>> TOTAL TIME 12.47 sec
Worker 1: 2025-12-19 21:16:44,963 [INFO] 100%|##########| 1/1 [00:12<00:00, 12.63s/it]
Worker 1: 2025-12-19 21:16:44,963 [INFO] 100%|##########| 1/1 [00:12<00:00, 12.63s/it]
Worker 1: 2025-12-19 21:16:44,964 [INFO] >>>> completed in 12.887 sec
```

No container appears during the run
<img width="1048" height="139" alt="image" src="https://github.com/user-attachments/assets/283a2233-07a9-4157-9e5f-5425cf5dee26" />

Container appears momentarily when analysis is stopped
<img width="1050" height="187" alt="image" src="https://github.com/user-attachments/assets/6347a7cf-9811-4642-bdaa-f3b097512883" />



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CellProfiler plugins (RunCellpose and Runilastik) working only in test mode and not in analysis mode using Docker Desktop in Windows computer #298

Running beginner segmentation bonus exercise pipeline with order of the modules slightly changed and an extra `OverlayOutlines` added

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CellProfiler plugins (RunCellpose and Runilastik) working only in test mode and not in analysis mode using Docker Desktop in Windows computer #298

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Running beginner segmentation bonus exercise pipeline with order of the modules slightly changed and an extra OverlayOutlines added

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Running beginner segmentation bonus exercise pipeline with order of the modules slightly changed and an extra `OverlayOutlines` added