microsam crashes when commit path is set #868

Jintram · 2025-02-18T11:22:44Z

Hi microsam team,

Great work, many thanks for this!

Just wanted to report a crash I experience:

When trying microsam with a simple example image of some fluorescently labeled cells, I can use everything with relative ease. (I'm now working through the tutorial & documentation.)
However, when I set a "commit path", and press "commit [c]", the program crashses.

Workflow:

I use the conda installation as in the documentation. I run python from terminal, and execute the following lines to get started:

# Libs
import napari
import numpy as np
from skimage import io

# Load example image
img_toseg = io.imread('/Users/m.wehrens/Data_UVA/example-datasets/HeLa-Cells-MW/example_cell_image.tif')
# Downsize image for ease of working
img_toseg_tile = img_toseg[:3000:2, :3000:2]
# Create the viewer and add the image
viewer = napari.view_image(np.log(img_toseg_tile), name='toseg_log', opacity=1)

Using plugins > microsam, I open the annotator 2D.
I compute embeddings using the "vit_t" model.
I add some rectangular prompts.
Press segment
When I commit without "commit path" set, it works fine.
When I commit with "commit path" set, the program crashes.

My system is the following:

System: Apple M4 Max (36 GB), MacOS: 15.1 (24B2082)

I get the following error report:

>>> 2025-02-18 12:10:48.758 python[5897:144028] The class 'NSOpenPanel' overrides the method identifier.  This method is implemented by class 'NSWindow'
Using apple MPS device.
Computed embeddings for vit_t
WARNING: Traceback (most recent call last):
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1279, in _run_emit_loop
    self._run_emit_loop_inner()
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1308, in _run_emit_loop_immediate
    caller.cb(args)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_weak_callback.py", line 358, in cb
    self._f(*self._args, *args, **self._kwargs)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 235, in _disable_button_and_call
    self.__call__()  # type: ignore [call-arg]
    ^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 351, in __call__
    value = self._function(*bound.args, **bound.kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 502, in commit
    _commit_to_file(commit_path, viewer, layer, seg, mask, bb)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 471, in _commit_to_file
    write_prompts(
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 442, in write_prompts
    g = f.create_group(f"prompts/{object_id}")
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/z5py/group.py", line 133, in create_group
    raise KeyError("An object with name %s already exists" % name)
KeyError: 'An object with name prompts/4 already exists'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py", line 69, in _on_value_change
    self.changed.emit(value)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1201, in emit
    self._run_emit_loop(args)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1296, in _run_emit_loop
    raise loop_err from cb_err  # emit() call ABOVE || callback error BELOW
    ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1279, in _run_emit_loop
    self._run_emit_loop_inner()
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1308, in _run_emit_loop_immediate
    caller.cb(args)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_weak_callback.py", line 358, in cb
    self._f(*self._args, *args, **self._kwargs)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 235, in _disable_button_and_call
    self.__call__()  # type: ignore [call-arg]
    ^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 351, in __call__
    value = self._function(*bound.args, **bound.kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 502, in commit
    _commit_to_file(commit_path, viewer, layer, seg, mask, bb)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 471, in _commit_to_file
    write_prompts(
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 442, in write_prompts
    g = f.create_group(f"prompts/{object_id}")
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/z5py/group.py", line 133, in create_group
    raise KeyError("An object with name %s already exists" % name)
psygnal.EmitLoopError: 

While emitting signal 'magicgui.widgets.PushButton.changed', an error occurred in a callback:

  KeyError: 'An object with name prompts/4 already exists'
  --------------------------------------------------------

  SIGNAL EMISSION: 
    /Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py:69 in _on_value_change
      self.changed.emit(value)  # <-- SIGNAL WAS EMITTED HERE

  CALLBACK CHAIN:
    /Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py:235 in _disable_button_and_call
    ... 4 more frames ...
    /Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/z5py/group.py:133 in create_group
      raise KeyError("An object with name %s already exists" % name)  # <-- ERROR OCCURRED HERE 

      Local variables:
                name = 'prompts/4'
WARNING:vispy:Traceback (most recent call last):
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1279, in _run_emit_loop
    self._run_emit_loop_inner()
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1308, in _run_emit_loop_immediate
    caller.cb(args)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_weak_callback.py", line 358, in cb
    self._f(*self._args, *args, **self._kwargs)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 235, in _disable_button_and_call
    self.__call__()  # type: ignore [call-arg]
    ^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 351, in __call__
    value = self._function(*bound.args, **bound.kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 502, in commit
    _commit_to_file(commit_path, viewer, layer, seg, mask, bb)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 471, in _commit_to_file
    write_prompts(
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 442, in write_prompts
    g = f.create_group(f"prompts/{object_id}")
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/z5py/group.py", line 133, in create_group
    raise KeyError("An object with name %s already exists" % name)
KeyError: 'An object with name prompts/4 already exists'

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py", line 69, in _on_value_change
    self.changed.emit(value)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1201, in emit
    self._run_emit_loop(args)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1296, in _run_emit_loop
    raise loop_err from cb_err  # emit() call ABOVE || callback error BELOW
    ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1279, in _run_emit_loop
    self._run_emit_loop_inner()
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_signal.py", line 1308, in _run_emit_loop_immediate
    caller.cb(args)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/psygnal/_weak_callback.py", line 358, in cb
    self._f(*self._args, *args, **self._kwargs)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 235, in _disable_button_and_call
    self.__call__()  # type: ignore [call-arg]
    ^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py", line 351, in __call__
    value = self._function(*bound.args, **bound.kwargs)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 502, in commit
    _commit_to_file(commit_path, viewer, layer, seg, mask, bb)
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 471, in _commit_to_file
    write_prompts(
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/micro_sam/sam_annotator/_widgets.py", line 442, in write_prompts
    g = f.create_group(f"prompts/{object_id}")
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/z5py/group.py", line 133, in create_group
    raise KeyError("An object with name %s already exists" % name)
psygnal.EmitLoopError: 

While emitting signal 'magicgui.widgets.PushButton.changed', an error occurred in a callback:

  KeyError: 'An object with name prompts/4 already exists'
  --------------------------------------------------------

  SIGNAL EMISSION: 
    /Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/bases/_value_widget.py:69 in _on_value_change
      self.changed.emit(value)  # <-- SIGNAL WAS EMITTED HERE

  CALLBACK CHAIN:
    /Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/magicgui/widgets/_function_gui.py:235 in _disable_button_and_call
    ... 4 more frames ...
    /Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/site-packages/z5py/group.py:133 in create_group
      raise KeyError("An object with name %s already exists" % name)  # <-- ERROR OCCURRED HERE 

      Local variables:
                name = 'prompts/4'
zsh: abort      python
/Users/m.wehrens/miniconda3/envs/2025_microsam/lib/python3.11/multiprocessing/resource_tracker.py:254: UserWarning: resource_tracker: There appear to be 1 leaked semaphore objects to clean up at shutdown
  warnings.warn('resource_tracker: There appear to be %d '

anwai98 · 2025-02-18T11:59:13Z

Hi @Jintram,

Thanks for your interest in micro-sam. The feature to store the committed prompts is still a WIP (see #408). It's good that you reported the issue, we will investigate this and come back to you!

In general, is this a feature you are interest in for some specific reason? (if not, I suggest to avoid committing the prompts for now and continue with your segmentation workflow).

Let me know if you come across any other issues!

Jintram · 2025-02-18T12:17:23Z

Hi Anwai,

Thanks for your very fast reply!

In general, is this a feature you are interest in for some specific reason?

I am still in the stage were I'm trying to figure out how your software works (going through the tutorials right now), and I thought that the "commit path" would allow me to save the segmentation, similar to the "embeddings save path" (which is a really convenient feature if I want to quickly show microsam features to other people, or continue working on a segmentation later).

However, I now realize I can save my segmentation in a better way, via the menu and "file > save selected layers".

In general, I was using the "commit" feature as this was suggested in the Youtube tutorial video:

https://youtu.be/9xjJBg_Bfuc?si=_Pp9-XR-Ig3QGpEY&t=727

Some context: In the future, I was also hoping to potentially apply some transfer learning to tune the model further for my own dataset. But I really have to delve into this subject matter further. That's the reason I was diligently following the tutorial for now. I see there's also notes about this in the documentation (https://computational-cell-analytics.github.io/micro-sam/micro_sam.html#fine-tuning-questions). But I think this is probably unrelated to this current issue.

Anyways, many thanks for your quick answer!

Best, Martijn

constantinpape · 2025-02-18T14:47:46Z

Thank you for the report and context @Jintram ! We will look into fixing the commit path in one of the next releases.

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microsam crashes when commit path is set #868

microsam crashes when commit path is set #868

Jintram commented Feb 18, 2025

anwai98 commented Feb 18, 2025

Jintram commented Feb 18, 2025

constantinpape commented Feb 18, 2025

microsam crashes when commit path is set #868

microsam crashes when commit path is set #868

Comments

Jintram commented Feb 18, 2025

anwai98 commented Feb 18, 2025

Jintram commented Feb 18, 2025

constantinpape commented Feb 18, 2025