ctrl + c ctrl + v doesn't work

[soldevilaaron-creator]

Is there an existing issue for this?

• I have searched the existing issues

Operating System

Edition Windows 11 Pro
Version 25H2
OS build 26200.8246
Experience Windows Feature Experience Pack 1000.26100.297.0

DeepLabCut version

'3.0.0rc13'

What engine are you using?

pytorch

DeepLabCut mode

single animal

Device type

CPU: AMD Ryzen 7 9700X 8-Core Processor (3.80 GHz)
GPU: NVIDIA GeForce RTX 5070 (12 GB)

Bug description 🐛

I was analysing Elevated Plus Maze videos and wanted to add the shape of the EPM to each frame. Since the EPM doesn't move I marked the point in the first frame then I wanted to copy them to the others. (I want to do this because the EPM isn't in the same location in each video, teaching DLC to recognise it I hope will solve issues with small variations in its placement, e.g.: if I knock over the camera a little. If someone knows a better way to do this with DLC, I'm all ears though.) A sidenote: I decided to add the EPM to the skeleton structure after I analysed the mouse movements and realised alternative ways of marking the EPM shape weren't as reliable as I tought they wouldbe.

Steps To Reproduce

Cuda version:
release 13.0, V13.0.88
Build cuda_13.0.r13.0/compiler.36424714_0
DLC version:
3.0.0rc13
pytorch version:
2.12.0.dev20260327+cu128
I opened a mp4 file from labeled-data then started adding the new bodyparts. After I selected all points with ctrl + a, I pressed ctrl + c, moved on the next frame with the right arrow key and pressed ctrl + v. When I pressed ctrl + v the error message showed up, see the relevant log output below.

Relevant log output

Error calling Python override of QSplitter::keyPressEvent(): Traceback (most recent call last):
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari\_qt\qt_viewer.py", line 1173, in keyPressEvent
    self.canvas._scene_canvas._backend._keyEvent(
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\vispy\app\backends\_qt.py", line 676, in _keyEvent
    vispy_event = func(native=ev, key=key, text=str(ev.text()), modifiers=mod)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\vispy\util\event.py", line 453, in __call__
    self._invoke_callback(cb, event)
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\vispy\util\event.py", line 471, in _invoke_callback
    _handle_exception(self.ignore_callback_errors,
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\vispy\util\event.py", line 469, in _invoke_callback
    cb(event)
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari\utils\key_bindings.py", line 512, in on_key_press
    event.handled = self.press_key(kb)
                    ^^^^^^^^^^^^^^^^^^
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari\utils\key_bindings.py", line 428, in press_key
    generator_or_callback = func()
                            ^^^^^^
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari\layers\points\_points_key_bindings.py", line 66, in paste
    layer._paste_data()
  File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\_widgets.py", line 249, in _paste_data
    offset = [self._slice_input[i] - self._clipboard["indices"][i] for i in not_disp]
              ~~~~~~~~~~~~~~~~~^^^
TypeError: '_SliceInput' object is not subscriptable

Anything else?

Thanks ahead for your help!

Code of Conduct

• I agree to follow this project's Code of Conduct

[C-Achard]

Hello @soldevilaaron-creator, thanks for reporting this.

The particular issue should be fixed in the refactored version, which you can install in your conda env with:

pip install shiboken6>=6.4.2
pip install git+https://github.com/DeepLabCut/napari-deeplabcut.git@refs/pull/183/head

If there are any issues, please revert to the current release with :

pip install napari-deeplabcut==0.2.1.8

Please let me know if there are any further issues with the copy-paste function there.

Best,
Cyril

[soldevilaaron-creator]

Thank you, the issue is fixed, the commands work now!

[soldevilaaron-creator]

Dear C-Achard!

Another problem presented itself, It may be connected to this one so I decided to reopen this issue, though maybe I am wrong. If I am, I can open a new issue. Everything is the same as before, and the ctrl + c ctrl + v function works. However, the new issue is that at some point deeplabcut forces my single animal project into a multi animal project, this prevents me from working further with my data.
I couldn't figure out where the issue is coming from, but it may be reproduced in the folowing way: create any new single animal project and add a random video to it. Extract then label the frames, if you continue the pipeline this way, nothing should happen. However, if you decide to open the config file and add a new bodypart, everything will change. To add only the new bodypart and keep the old ones, open napari, with ctrl + o open the config file then with ctrl + shift + o open the experiment/labeled-data/video/ folder and add the new labels. Save, exit, then in the DLC GUI run Create training dataset, the files it will create will be considered a multi-animal project.
Perhaps the relabeling process itself forced the multianimal project as when I opened it with it, I saw 2 point layers in addition to the image layer instead of 1 image and 1 point layer. Going back to the experiment/labeled-data/video folder, several things changed. When I open the csv file, the identity row appeared and when I opened the hdf5 file (with hdf view) block_0_items_level1 became an empty object (one of its attributes is block_0items_nameindividuals). When I look into the folder I can also see a json file in addition to the hdf5 and csv ones. Before adding the bodyparts to the config file, there was no json file, no identity row in excel and block_0_items_level1 contained the list of bodyparts in the hdf5 file.

I'm lost as to what I should do now, if I take my data to a new project the issue persists since as far as I can tell DLC uses the hdf5 file and not the csv (or not only the csv). Should I try to change the hdf5 files to solve the issue? How should I handle it in the future when I will get new videos to analyse? Or should I start again from scratch and relabel everything? I must have made the mistake when I analysed the videos with the new bodyparts what should have I done differently?

Thank you for your help in advance,
Soldevila Áron

[C-Achard]

Hello again @soldevilaaron-creator, no worries, happy to help!

Thanks for the very precise reproducing steps, I was able to isolate and fix the issue.
The bug was in the save path: single-animal data was normalized internally to enable safe dataframe comparisons in the plugin, but then was written back to disk in that multi-animal-shaped format instead of being rewritten back to the single-animal format.
Since the saved annotation file ended up with a multi-animal-style column structure, DLC later treated the training dataset as multi-animal.

The fixed version should be more robust, using the config first if available to determine if the project is multi-animal, and otherwise deriving from data format. Re-saving the layer with the fixed version should rewrite the affected annotation files back to the expected single-animal format. This has been tested locally on an example project and I've added some regression tests.

Regarding your data, no need to re-label or edit the h5, I can suggest the following options:

• If you don't mind staying on the experimental/preview version for now, update to:
  • pip install git+https://github.com/DeepLabCut/napari-deeplabcut.git@refs/pull/186/head
  • Please make a backup copy of the project (or at least the affected labeled-data/video/ folder) first.
  • Load the labeled data folder as usual
  • And save the layer once
  • Close the napari viewer fully
  • When loading the project again, the labeled data folder should be single-animal again

NOTE: this only affects the h5. Please generate any downstream/training data again from the h5 afterwards, otherwise they will still be multi-animal

• If you would like to go back to the current release, please re-install with:
  • pip install napari-deeplabcut==0.2.1.8
  • Then please send me the data folder in question, which I will convert back to single animal manually, since this was an experimental version bug I'm happy to fix it directly

Thanks again, and hope this helps!

Best,
Cyril

[soldevilaaron-creator]

Dear Cyril,

I updated DLC, opened napari, loaded in the config then opened the folder, but I couldn't save it. When I opened the folders to be labeled, I couldn't see any of the labels I placed. This is strange because the data is still there in the csv and hdf5 files. When I tried to save regardless, I got the folowing error message:
16:07:24 : DEBUG : MainThread : Lifecycle manager adopting existing layers count=1
16:07:24 : DEBUG : MainThread : Lifecycle manager adopt layer='CollectedData_Bautista_Soldevila_Aron' type=Points index=0
16:07:24 : DEBUG : MainThread : Setup points layer='CollectedData_Bautista_Soldevila_Aron' metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'kind', 'paths', 'project']
16:07:24 : DEBUG : MainThread : Wire points layer='CollectedData_Bautista_Soldevila_Aron' existing_store=True project=C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11 root=None len_paths=0
16:07:24 : DEBUG : MainThread : Setup points layer='CollectedData_Bautista_Soldevila_Aron' allow_merge=False metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'kind', 'paths', 'project']
16:07:36 : ERROR : MainThread : Key 'df_with_missing' not found in C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m88_2025-10-14 16-21-54_labeled\CollectedData_Bautista_Soldevila_Aron.h5. Trying to read without specifying a key.
16:07:36 : DEBUG : MainThread : Lifecycle manager processing insert layer='images' type=Image index=1
16:07:36 : DEBUG : MainThread : Setup image layer='images' index=1 reorder=True paths_count=50 root='C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m88_2025-10-14 16-21-54_labeled' context_changed=True
16:07:36 : DEBUG : MainThread : Remap start layer='CollectedData_Bautista_Soldevila_Aron' old_paths_len=50 new_paths_len=50 data_shape=(0, 3) frame_min=None frame_max=None
16:07:36 : DEBUG : MainThread : Remap result layer='CollectedData_Bautista_Soldevila_Aron' changed=False mapped_count=50 depth=3 message=Path keys already aligned; no remap needed. warnings=()
16:07:36 : DEBUG : MainThread : Remap accepted-noop for CollectedData_Bautista_Soldevila_Aron (depth=3, mapped=50): Path keys already aligned; no remap needed.
16:07:36 : DEBUG : MainThread : on_active_layer_change value=None took 0.161 ms
16:07:36 : DEBUG : MainThread : on_active_layer_change value='images' took 0.071 ms
16:07:36 : DEBUG : MainThread : on_active_layer_change value='images' took 0.074 ms
16:07:37 : DEBUG : MainThread : Lifecycle manager processing insert layer='CollectedData_Bautista_Soldevila_Aron [1]' type=Points index=2
16:07:37 : DEBUG : MainThread : Setup points layer='CollectedData_Bautista_Soldevila_Aron [1]' metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'source_h5', 'source_h5_name', 'source_h5_stem']
16:07:37 : DEBUG : MainThread : Wire points layer='CollectedData_Bautista_Soldevila_Aron [1]' existing_store=True project=None root=C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m88_2025-10-14 16-21-54_labeled len_paths=50
16:07:37 : DEBUG : MainThread : Setup points layer='CollectedData_Bautista_Soldevila_Aron [1]' allow_merge=True metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'source_h5', 'source_h5_name', 'source_h5_stem']
16:07:37 : DEBUG : MainThread : Remap start layer='CollectedData_Bautista_Soldevila_Aron' old_paths_len=50 new_paths_len=50 data_shape=(0, 3) frame_min=None frame_max=None
16:07:37 : DEBUG : MainThread : Remap result layer='CollectedData_Bautista_Soldevila_Aron' changed=False mapped_count=50 depth=3 message=Path keys already aligned; no remap needed. warnings=()
16:07:37 : DEBUG : MainThread : Remap accepted-noop for CollectedData_Bautista_Soldevila_Aron (depth=3, mapped=50): Path keys already aligned; no remap needed.
16:07:37 : DEBUG : MainThread : Remap start layer='CollectedData_Bautista_Soldevila_Aron [1]' old_paths_len=50 new_paths_len=50 data_shape=(800, 3) frame_min=0 frame_max=49
16:07:37 : DEBUG : MainThread : Remap result layer='CollectedData_Bautista_Soldevila_Aron [1]' changed=False mapped_count=50 depth=3 message=Path keys already aligned; no remap needed. warnings=()
16:07:37 : DEBUG : MainThread : Remap accepted-noop for CollectedData_Bautista_Soldevila_Aron [1] (depth=3, mapped=50): Path keys already aligned; no remap needed.
16:07:37 : DEBUG : MainThread : on_active_layer_change value=None took 0.118 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value='CollectedData_Bautista_Soldevila_Aron [1]' took 1.954 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value='CollectedData_Bautista_Soldevila_Aron [1]' took 0.753 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value=None took 0.142 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value='images' took 0.070 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value=None took 0.107 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value='CollectedData_Bautista_Soldevila_Aron' took 1.086 ms
16:07:37 : DEBUG : MainThread : on_active_layer_change value='CollectedData_Bautista_Soldevila_Aron' took 0.412 ms
16:07:42 : DEBUG : MainThread : About to save. io.kind=None save_target=None
16:07:42 : ERROR : MainThread : Failed to prepare save checks for layer 'CollectedData_Bautista_Soldevila_Aron'
Traceback (most recent call last):
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\ui\ui_dialogs\save.py", line 199, in _save_single_points_layer
report = compute_overwrite_report_for_points_save(layer.data, attributes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\core\conflicts.py", line 88, in compute_overwrite_report_for_points_save
df_new = form_df_from_validated(ctx)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\core\dataframes.py", line 289, in form_df_from_validated
guarantee_multiindex_rows(df)
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\core\dataframes.py", line 218, in guarantee_multiindex_rows
path = df.index[0]
~~~~~~~~^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\pandas\core\indexes\base.py", line 5401, in getitem
return getitem(key)
^^^^^^^^^^^^
IndexError: index 0 is out of bounds for axis 0 with size 0

Best,
Áron

[C-Achard]

Hello again @soldevilaaron-creator,

Sorry about that, could you try without loading the config first ?
The idea is to first get the project back to a regular single-animal format, which should be feasible by loading the labeled-data folder first, then saving the points layer, without having to add the config at all. If it does not load the data at all, see below.
Just to confirm:

• Are you loading only a single folder at a time?
• I would recommend not to load the config file yet
• If possible, please try on a data folder that is not affected by the single animal saving issue
• I have pushed some commits to this branch today, so I would recommend updating again: pip install git+https://github.com/DeepLabCut/napari-deeplabcut.git@refs/pull/186/head.

If you would like to later refresh the bodyparts list from config, then you could add it after loading the folder, but for now I would recommend saving the data once first.

The data should be fine, nothing has been written back yet (it fails before saving), so no worries.

If loading/saving fails

Please note, while I tested this locally, it may indeed not work for your project, and in this case the easiest would be to share the data, so I can check the format and ensure it is in proper single-animal format before sharing it back. This would let me test on a different kind of data, which is always welcome if possible.

If errors occur during loading, you can use the new debug log to send the traceback, for convenience:

If this is affecting a lot of your data, please send a small representative sample, and I can write a script to convert the rest of it back if needed.

Thanks,
Cyril

[soldevilaaron-creator]

Dear Cyril!

The recent update managed to get the pipeline working to some point. Below I will show the logs made available by the new function. There was, however, 1 exception, where performind the advised steps did nothing, I will show the error log from the terminal. Checking labels also works now. However, creating a training dataset doesn't work any more.
Log after saving "C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m195_2025-10-20 13-37-17_labeled" file:

Environment

• python: 3.12.13 | packaged by Anaconda, Inc. | (main, Mar 19 2026, 20:16:45) [MSC v.1942 64 bit (AMD64)]
• platform: Windows-11-10.0.26200-SP0
• napari-deeplabcut: 0.2.1.9.dev367+g104e4ee35
• napari: 0.6.6
• qtpy: 2.4.3
• PySide6: 6.11.0
• PyQt6: not-installed
• shiboken6: 6.11.0
• numpy: 1.26.4
• pydantic: 2.13.0b2
• plugin_module_path: C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut_init_.py

Viewer

• n_layers: 2
• active_layer: CollectedData_Bautista_Soldevila_Aron

Layers

• [1] name='images', type=Image, visible=True
  • data_shape: (50, 1041, 960, 3)
  • metadata_keys: ['dlc', 'paths', 'project', 'root']
  • property_keys: []
  • project: Deeplabcut/Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11
  • root: labeled-data/m195_2025-10-20 13-37-17_labeled
  • paths_count: 50
  • has_header: False
  • has_tables: False
  • has_save_target: False
• [2] name='CollectedData_Bautista_Soldevila_Aron', type=Points, visible=True
  • data_shape: (800, 3)
  • metadata_keys: ['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'shape', 'source_h5', 'source_h5_name', 'source_h5_stem']
  • property_keys: ['id', 'label', 'likelihood', 'valid']
  • project: None
  • root: labeled-data/m195_2025-10-20 13-37-17_labeled
  • paths_count: 50
  • has_header: True
  • has_tables: False
  • has_save_target: False

Recent plugin logs

14:25:50.255 (+     0.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Lifecycle manager adopting existing layers count=2
14:25:50.256 (+     1.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Lifecycle manager adopt layer='images' type=Image index=0
14:25:50.258 (+     3.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Setup image layer='images' index=0 reorder=True paths_count=50 root='C:\\Bautista_Soldevila_Aron\\Deeplabcut\\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\\labeled-data\\m195_2025-10-20 13-37-17_labeled' context_changed=True
14:25:50.258 (+     3.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Lifecycle manager adopt layer='CollectedData_Bautista_Soldevila_Aron' type=Points index=1
14:25:50.289 (+    33.9 ms) | DEBUG    | napari-deeplabcut._widgets | Setup points layer='CollectedData_Bautista_Soldevila_Aron' metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'shape', 'source_h5', 'source_h5_name', 'source_h5_stem']
14:25:50.290 (+    34.9 ms) | DEBUG    | napari-deeplabcut.lifecycle | Wire points layer='CollectedData_Bautista_Soldevila_Aron' existing_store=True project=None root=C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m195_2025-10-20 13-37-17_labeled len_paths=50
14:25:50.290 (+    34.9 ms) | DEBUG    | napari-deeplabcut.lifecycle | Setup points layer='CollectedData_Bautista_Soldevila_Aron' allow_merge=False metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'shape', 'source_h5', 'source_h5_name', 'source_h5_stem']
14:25:50.291 (+    35.9 ms) | DEBUG    | napari-deeplabcut.lifecycle | Remap start layer='CollectedData_Bautista_Soldevila_Aron' old_paths_len=50 new_paths_len=50 data_shape=(800, 3) frame_min=0 frame_max=49
14:25:50.291 (+    35.9 ms) | DEBUG    | napari-deeplabcut.lifecycle | Remap result layer='CollectedData_Bautista_Soldevila_Aron' changed=False mapped_count=50 depth=3 message=Path keys already aligned; no remap needed. warnings=()
14:25:50.291 (+    35.9 ms) | DEBUG    | napari-deeplabcut.lifecycle | Remap accepted-noop for CollectedData_Bautista_Soldevila_Aron (depth=3, mapped=50): Path keys already aligned; no remap needed.
14:25:53.255 (+  3000.0 ms) | DEBUG    | napari-deeplabcut._widgets | About to save. io.kind=<AnnotationKind.GT: 'gt'> save_target=None
14:25:53.559 (+  3304.0 ms) | DEBUG    | napari-deeplabcut._widgets | About to save. io.kind=<AnnotationKind.GT: 'gt'> save_target=None
14:25:53.816 (+  3561.0 ms) | DEBUG    | napari-deeplabcut._widgets | About to save. io.kind=<AnnotationKind.GT: 'gt'> save_target=None
14:25:54.056 (+  3801.2 ms) | DEBUG    | napari-deeplabcut._widgets | About to save. io.kind=<AnnotationKind.GT: 'gt'> save_target=None
14:26:19.145 (+ 28890.0 ms) | DEBUG    | napari-deeplabcut._widgets | About to save. io.kind=<AnnotationKind.GT: 'gt'> save_target=None

log after saving: "C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m195_2025-10-20 13-37-17"

Environment

• python: 3.12.13 | packaged by Anaconda, Inc. | (main, Mar 19 2026, 20:16:45) [MSC v.1942 64 bit (AMD64)]
• platform: Windows-11-10.0.26200-SP0
• napari-deeplabcut: 0.2.1.9.dev367+g104e4ee35
• napari: 0.6.6
• qtpy: 2.4.3
• PySide6: 6.11.0
• PyQt6: not-installed
• shiboken6: 6.11.0
• numpy: 1.26.4
• pydantic: 2.13.0b2
• plugin_module_path: C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut_init_.py

Viewer

• n_layers: 2
• active_layer: CollectedData_Bautista_Soldevila_Aron

Layers

• [1] name='images', type=Image, visible=True
  • data_shape: (50, 1041, 960, 3)
  • metadata_keys: ['dlc', 'paths', 'project', 'root']
  • property_keys: []
  • project: Deeplabcut/Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11
  • root: labeled-data/m195_2025-10-20 13-37-17
  • paths_count: 50
  • has_header: False
  • has_tables: False
  • has_save_target: False
• [2] name='CollectedData_Bautista_Soldevila_Aron', type=Points, visible=True
  • data_shape: (1436, 3)
  • metadata_keys: ['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'shape', 'source_h5', 'source_h5_name', 'source_h5_stem']
  • property_keys: ['id', 'label', 'likelihood', 'valid']
  • project: None
  • root: labeled-data/m195_2025-10-20 13-37-17
  • paths_count: 50
  • has_header: True
  • has_tables: False
  • has_save_target: False

Recent plugin logs

14:28:35.931 (+     0.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Lifecycle manager adopting existing layers count=2
14:28:35.931 (+     0.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Lifecycle manager adopt layer='images' type=Image index=0
14:28:35.933 (+     2.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Setup image layer='images' index=0 reorder=True paths_count=50 root='C:\\Bautista_Soldevila_Aron\\Deeplabcut\\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\\labeled-data\\m195_2025-10-20 13-37-17' context_changed=True
14:28:35.933 (+     2.0 ms) | DEBUG    | napari-deeplabcut.lifecycle | Lifecycle manager adopt layer='CollectedData_Bautista_Soldevila_Aron' type=Points index=1
14:28:35.966 (+    35.5 ms) | DEBUG    | napari-deeplabcut._widgets | Setup points layer='CollectedData_Bautista_Soldevila_Aron' metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'shape', 'source_h5', 'source_h5_name', 'source_h5_stem']
14:28:35.966 (+    35.5 ms) | DEBUG    | napari-deeplabcut.lifecycle | Wire points layer='CollectedData_Bautista_Soldevila_Aron' existing_store=True project=None root=C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m195_2025-10-20 13-37-17 len_paths=50
14:28:35.966 (+    35.5 ms) | DEBUG    | napari-deeplabcut.lifecycle | Setup points layer='CollectedData_Bautista_Soldevila_Aron' allow_merge=False metadata_keys=['colormap_name', 'config_colormap', 'face_color_cycles', 'header', 'io', 'kind', 'name', 'paths', 'root', 'shape', 'source_h5', 'source_h5_name', 'source_h5_stem']
14:28:35.967 (+    36.5 ms) | DEBUG    | napari-deeplabcut.lifecycle | Remap start layer='CollectedData_Bautista_Soldevila_Aron' old_paths_len=50 new_paths_len=50 data_shape=(1436, 3) frame_min=0 frame_max=49
14:28:35.967 (+    36.5 ms) | DEBUG    | napari-deeplabcut.lifecycle | Remap result layer='CollectedData_Bautista_Soldevila_Aron' changed=False mapped_count=50 depth=3 message=Path keys already aligned; no remap needed. warnings=()
14:28:35.967 (+    36.5 ms) | DEBUG    | napari-deeplabcut.lifecycle | Remap accepted-noop for CollectedData_Bautista_Soldevila_Aron (depth=3, mapped=50): Path keys already aligned; no remap needed.
14:28:37.089 (+  1158.5 ms) | DEBUG    | napari-deeplabcut._widgets | About to save. io.kind=<AnnotationKind.GT: 'gt'> save_target=None

outlier: "C:\Bautista_Soldevila_Aron\Deeplabcut\Elevated_Plus_Maze-Bautista_Soldevila_Aron-2026-03-11\labeled-data\m88_2025-10-14 16-21-54" its -labelled version works fine. This is the only file with this problem.

ValueError Traceback (most recent call last)
File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut_widgets.py:311, in KeypointControls.init..()
308 if "save selected layer" in action_name:
309 action.triggered.disconnect()
310 action.triggered.connect(
--> 311 lambda: self._save_layers_dialog(
self = <napari_deeplabcut._widgets.KeypointControls(0x1f112184660) at 0x000001F1165FF140> 312 selected=True,
313 )
314 )
315 elif "save all layers" in action_name:
316 self.viewer.window.file_menu.removeAction(action)

File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut_widgets.py:1161, in KeypointControls._save_layers_dialog(self=<napari_deeplabcut._widgets.KeypointControls(0x1f112184660)>, selected=True)
1159 def _save_layers_dialog(self, selected=False):
1160 """Save layers (all or selected) using the dedicated save workflow."""
-> 1161 outcome = self._save_workflow.save_layers(selected=selected)
self = <napari_deeplabcut._widgets.KeypointControls(0x1f112184660) at 0x000001F1165FF140>
self._save_workflow = <napari_deeplabcut.ui.ui_dialogs.save.PointsLayerSaveWorkflow object at 0x000001F11660A510>
selected = True 1162 if not outcome.saved:
1163 return

File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\ui\ui_dialogs\save.py:155, in PointsLayerSaveWorkflow.save_layers(self=<napari_deeplabcut.ui.ui_dialogs.save.PointsLayerSaveWorkflow object>, selected=True)
152 return SaveOutcome(saved=False)
154 if len(selected_layers) == 1 and isinstance(selected_layers[0], Points):
--> 155 return self._save_single_points_layer(selected_layers[0])
selected_layers = [<Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50>]
selected_layers[0] = <Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50>
self = <napari_deeplabcut.ui.ui_dialogs.save.PointsLayerSaveWorkflow object at 0x000001F11660A510> 157 return self._save_multiple_layers(selected=selected, selected_layers=selected_layers)

File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari_deeplabcut\ui\ui_dialogs\save.py:238, in PointsLayerSaveWorkflow._save_single_points_layer(self=<napari_deeplabcut.ui.ui_dialogs.save.PointsLayerSaveWorkflow object>, layer=<Points layer 'CollectedData_Bautista_Soldevila_Aron'>)
235 metadata_changed = save_metadata != dict(layer.metadata or {})
237 with _temporary_layer_metadata(layer, save_metadata):
--> 238 self.viewer.layers.save("dlc.h5", selected=True, plugin="napari-deeplabcut")
self = <napari_deeplabcut.ui.ui_dialogs.save.PointsLayerSaveWorkflow object at 0x000001F11660A510>
self.viewer.layers = [<Image layer 'images' at 0x1f104df9a90>, <Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50>]
self.viewer = Viewer(camera=Camera(center=(0.0, 485.5, 464.0), zoom=0.6135629709364908, angles=(0.0, 0.0, 90.0), perspective=0.0, mouse_pan=True, mouse_zoom=True, orientation=(<DepthAxisOrientation.TOWARDS: 'towards'>, <VerticalAxisOrientation.DOWN: 'down'>, <HorizontalAxisOrientation.RIGHT: 'right'>)), cursor=Cursor(position=(0.0, 547.4333665116296, 1228.3877590156014), viewbox=(0, 0), scaled=True, style=<CursorStyle.STANDARD: 'standard'>, size=1.0), dims=Dims(ndim=3, ndisplay=2, order=(0, 1, 2), axis_labels=('0', '1', '2'), rollable=(True, True, True), range=(RangeTuple(start=0.0, stop=49.0, step=1.0), RangeTuple(start=0.0, stop=971.0, step=1.0), RangeTuple(start=0.0, stop=928.0, step=1.0)), margin_left=(0.0, 0.0, 0.0), margin_right=(0.0, 0.0, 0.0), point=(0.0, 485.0, 464.0), last_used=0), grid=GridCanvas(stride=1, shape=(-1, -1), enabled=False, spacing=0.0), layers=[<Image layer 'images' at 0x1f104df9a90>, <Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50>], help='use <5> for transform, use <2> for add points, use <3> for select points', status={'layer_name': 'CollectedData_Bautista_Soldevila_Aron', 'layer_base': 'm88_2025-10-14 16-21-54', 'source_type': 'plugin', 'plugin': 'napari-deeplabcut', 'coordinates': ' [0 547 1228]: ', 'coords': ' [0 547 1228]', 'value': ''}, tooltip=Tooltip(visible=False, text=''), theme='dark', title='napari', mouse_over_canvas=True, mouse_move_callbacks=[], mouse_drag_callbacks=[<function drag_to_zoom at 0x000001F171D98040>], mouse_double_click_callbacks=[<function double_click_to_zoom at 0x000001F171D5FF60>], mouse_wheel_callbacks=[<function dims_scroll at 0x000001F171D5FEC0>], _persisted_mouse_event={}, _mouse_drag_gen={}, _mouse_wheel_gen={}, _keymap={}) 240 # Persist successful save-time metadata improvements into the live layer.
241 if metadata_changed:

File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari\components\layerlist.py:543, in LayerList.save(self=[<Image layer 'images' at 0x1f104df9a90>, <Point...dData_Bautista_Soldevila_Aron' at 0x1f114189e50>], path='dlc.h5', selected=True, plugin='napari-deeplabcut', _writer=None)
540 warnings.warn(msg)
541 return []
--> 543 return save_layers(path, layers, plugin=plugin, _writer=_writer)
layers = [<Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50>]
path = 'dlc.h5'
plugin = 'napari-deeplabcut'
_writer = None
File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari\plugins\io.py:244, in save_layers(path='dlc.h5', layers=[<Points layer 'CollectedData_Bautista_Soldevila_Aron'>], plugin='napari-deeplabcut', _writer=None)
240 written, writer_name = _write_multiple_layers_with_plugins(
241 path, layers, plugin_name=plugin, _writer=_writer
242 )
243 elif len(layers) == 1:
--> 244 _written, writer_name = _write_single_layer_with_plugins(
writer_name = ''
layers = [<Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50>]
path = 'dlc.h5'
plugin = 'napari-deeplabcut'
_writer = None
layers[0] = <Points layer 'CollectedData_Bautista_Soldevila_Aron' at 0x1f114189e50> 245 path, layers[0], plugin_name=plugin, _writer=_writer
246 )
247 written = [_written] if _written else []
248 else:

File ~\anaconda\envs\deeplabcut\Lib\site-packages\napari\plugins\io.py:475, in _write_single_layer_with_plugins(path='dlc.h5', layer=<Points layer 'CollectedData_Bautista_Soldevila_Aron'>, plugin_name='napari-deeplabcut', writer=None)
473 if plugin_name and (plugin_name not in plugin_manager.plugins):
474 names = {i.plugin_name for i in hook_caller.get_hookimpls()}
--> 475 raise ValueError(
trans = <napari.utils.translations.TranslationBundle object at 0x000001F164122240>
plugin_name = 'napari-deeplabcut'
names = set() 476 trans.(
477 "There is no registered plugin named '{plugin_name}'.\nPlugins capable of writing layer._type_string layers are: {names}",
478 deferred=True,
479 plugin_name=plugin_name,
480 names=names,
481 )
482 )
484 # Call the hook_caller
485 written_path: str | None = hook_caller(
486 _plugin=plugin_name,
487 path=abspath_or_url(path),
488 data=layer.data,
489 meta=layer._get_state(),
490 )

ValueError: There is no registered plugin named 'napari-deeplabcut'.
Plugins capable of writing layer._type_string layers are: set()

Dataset creation issue:
Traceback (most recent call last):
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\deeplabcut\gui\tabs\create_training_dataset.py", line 313, in create_training_dataset
deeplabcut.create_training_dataset(
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\deeplabcut\generate_training_dataset\trainingsetmanipulation.py", line 1045, in create_training_dataset
Data = merge_annotateddatasets(
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\deeplabcut\generate_training_dataset\trainingsetmanipulation.py", line 559, in merge_annotateddatasets
AnnotationData = pd.concat(AnnotationData).sort_index()
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\pandas\core\reshape\concat.py", line 395, in concat
return op.get_result()
^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\pandas\core\reshape\concat.py", line 680, in get_result
indexers[ax] = obj_labels.get_indexer(new_labels)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\pandas\core\indexes\base.py", line 3960, in get_indexer
return self._get_indexer(target, method, limit, tolerance)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\pandas\core\indexes\base.py", line 3981, in _get_indexer
tgt_values = engine._extract_level_codes( # type: ignore[union-attr]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pandas/_libs/index.pyx", line 752, in pandas._libs.index.BaseMultiIndexCodesEngine._extract_level_codes
File "C:\Users\solde\anaconda\envs\deeplabcut\Lib\site-packages\pandas\core\indexes\multi.py", line 2598, in _recode_for_new_levels
raise AssertionError(
AssertionError: Length of new_levels (4) must be <= self.nlevels (3)

Bests,
Áron