Crash during segmentation saving

[Kiskijavi]

Description:

After segmentation I cannot save the progress. I tried eliminating the objects touching the borders. Interestingly only happens in frame 341, before that frame I can save without problems.

2026-04-15_14-14-28_acdc_gui_06a3388a-5be7-40bc-ae84-652b36ee1758_stdout.log

Way to reproduce:

Segment up to frame 341.

Try to save.

(Optional) Link to data to reproduce error:

No response

Terminal output:

****************************************************************************************************
WARNING: Cell-ACDC is in error state. Please, restart.
****************************************************************************************************
[WARNING]: Saving process stopped because of critical error.
----------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/__init__.py", line 651, in inner_function
    result = func(self, *args, **kwargs)
  File "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/gui.py", line 17414, in workerCritical
    raise error
  File "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/workers.py", line 53, in run
    func(self)
  File "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/workers.py", line 6176, in run
    self.saveSegmData(posData, end_i, posData.segm_data)
  File "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/workers.py", line 6131, in saveSegmData
    saved_segm_data[frame_i] = lab
IndexError: index 340 is out of bounds for axis 0 with size 340

During handling of the above exception, another exception occurred:

----------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/gui.py", line 17424, in saveDataWorkerCritical
    self.worker.finished.emit()
RuntimeError: wrapped C/C++ object of type saveDataWorker has been deleted
Segmentation fault (core dumped)

Log file:

I cannot log it here so I will log it in the description.

Version information:

===============================================================================================================
Cell-ACDC info:

  - Version 1.7.1                                                                                              |
  - Released on: Wednesday 11 March 2026 at 10:43                                                              |
  - Installed in "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc"                  |
  - Environment folder: "/home/kiskijavi/miniforge3/envs/acdc"                                                 |
  - User profile folder: "/home/kiskijavi/acdc-appdata"                                                        |
  - Settings folder: "/home/kiskijavi/acdc-appdata/.acdc-settings"                                             |
  - Python 3.10.20                                                                                             |
  - Platform: Linux-6.17.0-22-generic-x86_64-with-glibc2.42                                                    |
  - System: Linux                                                                                              |
  - Linux distribution: Ubuntu 25.10 (Questing Quokka)                                                         |
  - Icons from: "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/cellacdc/qrc_resources.py"  |
  - Qt 6.6.0                                                                                                   |
  - Working directory: /home/kiskijavi                                                                         |
===============================================================================================================

==============================================================================================
SpotMAX info:

  - Version 1.2.4.dev6+g60d37414b                                                             |
  - Released on: Friday 13 March 2026 at 15:18                                                |
  - Installed in "/home/kiskijavi/miniforge3/envs/acdc/lib/python3.10/site-packages/spotmax"  |
  - Working directory: /home/kiskijavi                                                        |
==============================================================================================

[ElpadoCan]

Hi @Kiskijavi, I'm sorry to hear you are having issues, but we will look into this soon.

Unfortunately, I can only check this in a couple of days. Maybe @Teranis can have a look?

Thank you for your patience and for reporting this!

Best,
Francesco

[Teranis]

Hi @Kiskijavi , thanks for reporting this issue!

The problem was that posData.segm_data was too short since in the segmentation module, not all frames were segmented. We now extend saved_segm_data before saving with empty arrays.
Please use pip install --upgrade "git+https://github.com/SchmollerLab/Cell_ACDC.git" with your acdc environment active to update Cell-ACDC to the latest version available on GitHub.
Please let me know if there are any more issues. If your problem was resolved, please feel free to close this issue.

All the best,
Timon

[Kiskijavi]

Thank you @Teranis !

Indeed, updating the version did solve the problem. Yeah, at the beginning I chose to segment 340 frames but as I was going through it I changed my mind.

Best wishes,
Javier.