unable to stitch .ome.tif images taken be micromanager

[kvngvikram]

Hi,

I am trying to stitch multiple images taken in the form of grid by Micromanager. Attaching a sample data containing some 3x4=16 images.
The filenames have the grid location info, and there is metadata inside the images that I can't understand. I am attaching the dataset.
14_6.zip

I am getting the following error even for just two images.

$ ashlar '14_6_MMStack_New Grid 1-Grid_0_0.ome.tif' '14_6_MMStack_New Grid 1-Grid_0_1.ome.tif'
Stitching and registering input images
Cycle 0:
    reading 14_6_MMStack_New Grid 1-Grid_0_0.ome.tif
WARNING: A restricted method in java.lang.System has been called
WARNING: java.lang.System::load has been called by org.scijava.nativelib.NativeLibraryUtil in an unnamed module (file:/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/jars/bioformats_package.jar)
WARNING: Use --enable-native-access=ALL-UNNAMED to avoid a warning for callers in this module
WARNING: Restricted methods will be blocked in a future release unless native access is enabled

    assembling thumbnail 1/12/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/utils.py:202: FutureWarning: Parameter `area_threshold` is deprecated since version 0.26.0 and will be removed in 2.0.0 (or later). To avoid this warning, please use the parameter `max_size` instead. For more details, see the documentation of `remove_small_holes`. Note that the new threshold removes objects smaller than **or equal to** its value, while the previous parameter only removed smaller ones.
  mask = skimage.morphology.remove_small_holes(target != 0, hole_threshold)
    assembling thumbnail 2/12Traceback (most recent call last):
  File "/home/happy/installs_and_builds/micromamba/envs/temp/bin/ashlar", line 7, in <module>
    sys.exit(main())
             ^^^^^^
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/scripts/ashlar.py", line 226, in main
    return process_single(
           ^^^^^^^^^^^^^^^
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/scripts/ashlar.py", line 262, in process_single
    edge_aligner.run()
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/reg.py", line 509, in run
    self.make_thumbnail()
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/reg.py", line 521, in make_thumbnail
    self.reader.thumbnail = thumbnail.make_thumbnail(
                            ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/thumbnail.py", line 33, in make_thumbnail
    img = reader.read(c=channel, series=i)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/reg.py", line 452, in read
    img = self.reader.read(series, c)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/happy/installs_and_builds/micromamba/envs/temp/lib/python3.12/site-packages/ashlar/reg.py", line 414, in read
    img = np.frombuffer(byte_array.tostring(), dtype=dtype).reshape(shape)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: cannot reshape array of size 1203328 into shape (476,632)

Can you please help me out ...

Moreover, one suggestion about the installation, the installation downloads a bioformats_package.jar file during the installation. So for people working on offline computers not connected to the internet, just downloading the wheel file or source code and all the dependencies is not enough. Just a warning and hinting in which folder the file has to be copied will be helpful.

Thanks.