What is the best way to save image metadata alongside a tif?

Question

In my work as a grad student, I capture microscope images and use python to save them as raw tif's. I would like to add metadata such as the name of the microscope I am using, the magnification level, and the imaging laser wavelength. These details are all important for how I post-process the images.

I should be able to do this with a tif, right? Since it has a header?

I was able to add to the info in a PIL image:

im.info['microscope'] = 'george'

but when I save and load that image, the info I added is gone.

I'm open to all suggestions. If I have too, I'll just save a separate .txt file with the metadata, but it would be really nice to have it embedded in the image.

Answer 1

I should be able to do this with a tif, right? Since it has a header?

No.

First, your premise is wrong, but that's a red herring. TIFF does have a header, but it doesn't allow you to store arbitrary metadata in it.

But TIFF is a tagged file format, a series of chunks of different types, so the header isn't important here. And you can always create your own private chunk (any ID > 32767) and store anything you want there.

The problem is, nothing but your own code will have any idea what you stored there. So, what you probably want is to store EXIF or XMP or some other standardized format for extending TIFF with metadata. But even there, EXIF or whatever you choose isn't going to have a tag for "microscope", so ultimately you're going to end up having to store something like "microscope=george\nspam=eggs\n" in some string field, and then parse it back yourself.

But the real problem is that PIL/Pillow doesn't give you an easy way to store EXIF or XMP or anything else like that.

First, Image.info isn't for arbitrary extra data. At save time, it's generally ignored.

If you look at the PIL docs for TIFF, you'll see that it reads additional data into a special attribute, Image.tag, and can save data by passing a tiffinfo keyword argument to the Image.save method. But that additional data is a mapping from TIFF tag IDs to binary hunks of data. You can get the Exif tag IDs from the undocumented PIL.ExifTags.TAGS dict (or by looking them up online yourself), but that's as much support as PIL is going to give you.

Also, note that accessing tag and using tiffinfo in the first place requires a reasonably up-to-date version of Pillow; older versions, and classic PIL, didn't support it. (Ironically, they did have partial EXIF support for JPG files, which was never finished and has been stripped out…) Also, although it doesn't seem to be documented, if you built Pillow without libtiff it seems to ignore tiffinfo.

So ultimately, what you're probably going to want to do is:

• Pick a metadata format you want.
• Use a different library than PIL/Pillow to read and write that metadata. (For example, you can use GExiv2 or pyexif for EXIF.)