Extract Physical Pixel Size from SEM TIFF metadata.

[gyger]

Use Case

I use the library to open TIFF images create by SEM systems, in my Case FEI or now ThermoFischer. The tifffile library extracts the metadata but in AICSImageIO the metadata is only available in the numeric index {34680, 34682, 34683} depending on the tool.

For Zeiss this key would be {34118,}.

I am wondering if there is a wish to extract the physical pixel size from this metadata automatically and perhaps provide the metadata.

Solution

The physical pixel size is automatically read from the metadata in the TIFF file.

Alternatives

Create a new class basing on AICSImage, that sets the Physical Pixel size.

class SPMImage (aicsimageio.AICSImage):
   """
   """
   def __init__(self,         
               image: aicsimageio.types.ImageLike,
               reader: Optional[Type[aicsimageio.readers.reader.Reader]] = aicsimageio.readers.TiffReader,
               reconstruct_mosaic: bool = True,
               mask_nonvalid_data: bool = False,
               fs_kwargs: Dict[str, Any] = {},
               **kwargs: Any,):
      
      # Load Image
      super().__init__(image, reader, reconstruct_mosaic, fs_kwargs, **kwargs)
      self.mask_nonvalid_data = mask_nonvalid_data

      #FEI.
      fei_keys = {34680, 34682, 34683} & self.metadata.keys() # FEI_SFEG or FEI_HELIOS or FEI_TITAN
      if len(fei_keys) == 1: 
         self.metadata['FEI'] = self.metadata.pop(fei_keys.pop())
         self.reader._physical_pixel_sizes = aicsimageio.types.PhysicalPixelSizes(None, 
                                                                                  self.metadata['FEI']['Scan']['PixelHeight'], 
                                                                                  self.metadata['FEI']['Scan']['PixelWidth'])
         
      zeiss_keys = {34118,} & self.metadata.keys() # Carl Zeiss SEM
      if len(zeiss_keys) == 1: 
         self.metadata['ZEISS'] = self.metadata.pop(zeiss_keys.pop())

      self.metadata['DatabarHeight'] = self.metadata['FEI']['PrivateFei']['DatabarHeight']

[toloudis]

Thank you for this issue. I suggest looking at
https://github.com/bioio-devs/bioio-tifffile/blob/main/bioio_tifffile/reader.py#L579
and maybe you can make a pull request that modifies that file to add a check for these specific fields.
If it is possible for you, we suggest migrating to bioio as aicsimageio is in maintenance mode.
The api is basically the same and migration should be fairly easy.