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aelefebv / nellie

Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
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Unable to upload raw data due to dimension error #14

Closed EntoSanchez closed 5 months ago

EntoSanchez commented 5 months ago

I am trying to select files with known dimensions. The pixel information is included in the files based on what FIJI is showing when I click properties; however, when I try to upload to nellie, it says "no X dimension found"

188 if self.dim_sizes['X'] is None:
189     logger.error('No X dimension found.')

--> 190 raise ValueError 191 if self.dim_sizes['X'] != self.dim_sizes['Y']: 192 logger.warning('X and Y dimensions do not match. Non-square pixels not supported, ' 193 'so unexpected results and wrong measurements will occur.')

aelefebv commented 5 months ago

Hi Ento, any chance you can send me an example file that is creating this error to austin.e.lefebvre@gmail.com This will help me debug it.

EntoSanchez commented 5 months ago

Sent it!

aelefebv commented 5 months ago

Just figured out the issue, it seems like for whatever reason the file has only some parts of the dimensions info in the imagej metadata, but we need to go to the tif tags to pull out the rest. In any case, I'll push an update soon, and it should work with no issue! (but let me know if you do run into issues)