Getting ValueError: Incompatible shapes (266, 395, 164) != (44, 65, 82) for the source Tif-Source(44, 65, 82)

[michaelmell]

Dear Christoph,

We would like to evaluate ClearMap 2.1 for use in our imaging facility.

We were able to set it up and are able to start the GUI (clearmap-ui) and work through workflow steps.

However, at the registration step processing starts but then we get this error (see full logs below):

ValueError: Incompatible shapes (266, 395, 164) != (44, 65, 82) for the source Tif-Source(44, 65, 82)

I have looked at the code and searched online, but I am unable to find the cause of the problem.

Any support or input on this issue would be greatly appreciated!

Thank you in advance and kind regards,
Michael Mell

This

Invalid orientation, keeping current


Workspace[CellMap]{/home/DATA/<USER_NAME>/18531 tif series}
              raw: 18531_c1/20250805_DON-18531_5x_488_640_C1_Z<Z,3>.npy {409 files, ('Z',): (0,) -> (408,)}
                   18531_c1/20250805_DON-18531_5x_488_640_C1_Z<Z,3>.tif {409 files, ('Z',): (0,) -> (408,)}
 autofluorescence: 18531_c0/20250805_DON-18531_5x_488_640_C0_Z<Z,3>.tif {409 files, ('Z',): (0,) -> (408,)}
         stitched: stitched.npy
           layout: no file
       background: no file
        resampled: resampled.tif
                   resampled_autofluorescence.tif
resampled_to_auto: no file
auto_to_reference: no file
            cells: no file
          density: no file
   tile_extension: no file



Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_annotation_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_hemispheres_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_reference_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_distance_to_surface_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Could not find different channels in Pattern 20250805_DON-18531_5x_488_640_C0_Z???.tif


Could not find different channels in Pattern 20250805_DON-18531_5x_488_640_C1_Z???.tif


Workspace[CellMap]{/home/DATA/<USER_NAME>/18531 tif series}
              raw: 18531_c1/20250805_DON-18531_5x_488_640_C1_Z<Z,3>.npy {409 files, ('Z',): (0,) -> (408,)}
                   18531_c1/20250805_DON-18531_5x_488_640_C1_Z<Z,3>.tif {409 files, ('Z',): (0,) -> (408,)}
 autofluorescence: 18531_c0/20250805_DON-18531_5x_488_640_C0_Z<Z,3>.tif {409 files, ('Z',): (0,) -> (408,)}
         stitched: stitched.npy
           layout: no file
       background: no file
        resampled: resampled.tif
                   resampled_autofluorescence.tif
resampled_to_auto: no file
auto_to_reference: no file
            cells: no file
          density: no file
   tile_extension: no file



Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_annotation_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_hemispheres_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_reference_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_distance_to_surface_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Workspace[CellMap]{/home/DATA/<USER_NAME>/18531 tif series}
              raw: 18531_c1/20250805_DON-18531_5x_488_640_C1_Z<Z,3>.npy {409 files, ('Z',): (0,) -> (408,)}
                   18531_c1/20250805_DON-18531_5x_488_640_C1_Z<Z,3>.tif {409 files, ('Z',): (0,) -> (408,)}
 autofluorescence: 18531_c0/20250805_DON-18531_5x_488_640_C0_Z<Z,3>.tif {409 files, ('Z',): (0,) -> (408,)}
         stitched: stitched.npy
           layout: no file
       background: no file
        resampled: resampled.tif
                   resampled_autofluorescence.tif
resampled_to_auto: no file
auto_to_reference: no file
            cells: no file
          density: no file
   tile_extension: no file



Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_annotation_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_hemispheres_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_reference_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_distance_to_surface_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_annotation_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_hemispheres_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_reference_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


Preparing: '/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Resources/Atlas/ABA_25um_2017_distance_to_surface_-1_2_3__slice_None_None_None__slice_None_None_None__slice_None_None_None__.tif'


Atlas file exists, skipping


[LINES ELLIDED]


Process   396: Resampling: resampling axes (0, 1), slice (396,) / 409
Process   398: Resampling: resampling axes (0, 1), slice (398,) / 409
Process   399: Resampling: resampling axes (0, 1), slice (399,) / 409
Process   397: Resampling: resampling axes (0, 1), slice (397,) / 409
Process   400: Resampling: resampling axes (0, 1), slice (400,) / 409
Process   402: Resampling: resampling axes (0, 1), slice (402,) / 409
Process   403: Resampling: resampling axes (0, 1), slice (403,) / 409
Process   401: Resampling: resampling axes (0, 1), slice (401,) / 409
Process   404: Resampling: resampling axes (0, 1), slice (404,) / 409
Process   405: Resampling: resampling axes (0, 1), slice (405,) / 409
Process   407: Resampling: resampling axes (0, 1), slice (407,) / 409
Process   408: Resampling: resampling axes (0, 1), slice (408,) / 409
Process   406: Resampling: resampling axes (0, 1), slice (406,) / 409
   
MM-NOTE: Finishes successfully

[LINES ELLIDED]


Process   262: Resampling: resampling axes (1, 2), slice (262,) / 266
Process   263: Resampling: resampling axes (1, 2), slice (263,) / 266
Process   265: Resampling: resampling axes (1, 2), slice (265,) / 266
Process   264: Resampling: resampling axes (1, 2), slice (264,) / 266

MM-NOTE: Finishes successfully
   
[LINES ELLIDED]


Process   403: Resampling: resampling axes (0, 1), slice (403,) / 409
Process   404: Resampling: resampling axes (0, 1), slice (404,) / 409
Process   405: Resampling: resampling axes (0, 1), slice (405,) / 409
Process   406: Resampling: resampling axes (0, 1), slice (406,) / 409
Process   407: Resampling: resampling axes (0, 1), slice (407,) / 409
Process   408: Resampling: resampling axes (0, 1), slice (408,) / 409


Traceback (most recent call last):
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/gui/tabs.py", line 606, in run_registration
    self.main_window.wrap_in_thread(self.preprocessor.resample_for_registration, force=True)
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/gui/run_gui.py", line 619, in wrap_in_thread
    return result.get()
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/processors/sample_preparation.py", line 610, in resample_for_registration
    self.__resample_autofluorescence()
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/processors/sample_preparation.py", line 577, in __resample_autofluorescence
    result = resampling.resample(self.filename('autofluorescence'),
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/Alignment/Resampling.py", line 421, in resample
    resampled = io.initialize(source=sink, shape=sink_shape, dtype=dtype, as_source=True)
  File "/opt/clearmap/clearmap-ui-basic/.pixi/envs/default/lib/python3.9/site-packages/ClearMap/IO/IO.py", line 541, in initialize
    raise ValueError('Incompatible shapes %r != %r for the source %r!' % (shape, source.shape, source));
ValueError: Incompatible shapes (266, 395, 164) != (44, 65, 82) for the source Tif-Source(44, 65, 82)[uint16]{/home/DATA/<USER_NAME>/18531 tif series/resampled_autofluorescence.tif}!

[crousseau]

Hi @michaelmell thanks for reaching out,
Could you please post (or reach privately if you prefer)

• the metadata of the images (shape, dtype (16bit tiff ?))
• config files (sample and registration).

I don't see anything obvious from this angle but maybe I could see something in the parameters (e.g. what the "incompatible shapes" correspond to based on source shape and resampling factors).
Thanks, Charly