Tifffile is one option for saving microscopy images with lots of metadata in python.
It doesn't have a lot of external documentation, but the docstings are great so you can get a lot of info just by typing help(tifffile) in python, or go look at the source code.
You can look at the TiffWriter.save function in the source code (line 750) for the different keyword arguments you can use to write metadata.
One is to use description, which accepts a string. It will show up as the tag "ImageDescription" when you read your image.
Another is to use the extratags argument, which accepts a list of tuples. That allows you to write any tag name that exist in TIFF.TAGS(). One of the easiest way is to write them as strings because then you don't have to specify length.
You can also write ImageJ metadata with ijmetadata, for which the acceptable types are listed in the source code here.
As an example, if you write the following:
import json
import numpy as np
import tifffile
im = np.random.randint(0, 255, size=(150, 100), dtype=np.uint8)
# Description
description = "This is my description"
# Extratags
metadata_tag = json.dumps({"ChannelIndex": 1, "Slice": 5})
extra_tags = [("MicroManagerMetadata", 's', 0, metadata_tag, True),
("ProcessingSoftware", 's', 0, "my_spaghetti_code", True)]
# ImageJ metadata. 'Info' tag needs to be a string
ijinfo = {"InitialPositionList": [{"Label": "Pos1"}, {"Label": "Pos3"}]}
ijmetadata = {"Info": json.dumps(ijinfo)}
# Write file
tifffile.imsave(
save_name,
im,
ijmetadata=ijmetadata,
description=description,
extratags=extra_tags,
)
You can see the following tags when you read the image:
frames = tifffile.TiffFile(save_name)
page = frames.pages[0]
print(page.tags["ImageDescription"].value)
Out: 'this is my description'
print(page.tags["MicroManagerMetadata"].value)
Out: {'ChannelIndex': 1, 'Slice': 5}
print(page.tags["ProcessingSoftware"].value)
Out: my_spaghetti_code