PythonForAivia 2D+T not loaded back into Aivia correctly

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?

Apr 28 '20 11:04 tlancon

Need to test in:

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

Apr 28 '20 12:04 tlancon

Specifying the axes for each case seems the most reproducible. Though, some scripts would use the function to write ome-xml metadata that Aivia would read fine. See function "create_aivia_tif_xml_metadata" in: https://github.com/AiviaCommunity/PythonForAivia/blob/master/Recipes/ConvertImagesForAivia/Converter_Evos.py

Dec 02 '24 15:12 pmascalchi