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2D+T not loaded back into Aivia correctly #12

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tlancon opened this issue Apr 28, 2020 · 1 comment
Open

2D+T not loaded back into Aivia correctly #12

tlancon opened this issue Apr 28, 2020 · 1 comment
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@tlancon
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tlancon commented Apr 28, 2020

Need to specify axes using imsave

Example with skimage:
skimage.io.imsave(resultLocation, outputData, None, {'axes':'XYZ'})

Example with tifffile:
tifffile.imsave(f"{outpath}/my_TZCYX_data.tif", data, metadata={'axes': 'TZCYX'})

Do we need to say which axes are present for each case, or can we always use the TZYX format even if those aren't present?
@tlancon tlancon added the bug Something isn't working label Apr 28, 2020
@tlancon tlancon mentioned this issue Apr 28, 2020
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tlancon added a commit that referenced this issue Apr 28, 2020
@tlancon
Fixes 2D+T handling
fff7b4a 
Now updated to handle 2D+T correctly using 'axes' metadata parameter of tifffile.imwrite #12
@tlancon
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tlancon commented Apr 28, 2020

Need to test in:

  • Skeletonize
  • Morphological Texture
  • Max Slices
  • Min Slices
  • Meijering Neuriteness
  • Max Mask
  • Adjust Sigmoid
  • Adjust Gamma

seismonastic pushed a commit that referenced this issue Jun 17, 2020
@tlancon
Fixes 2D+T handling
cb08505 
Now updated to handle 2D+T correctly using 'axes' metadata parameter of tifffile.imwrite #12
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@tlancon