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Sam Desmond Schulman
Sam Desmond Schulman

Posted on Edited on AI-assisted

Read the TIFF metadata before you measure anything

#python #tutorial #science

I wrote this post with help from an AI writing tool.

An easy mistake in microscopy image analysis is trusting the file name. The information that matters for a measurement (pixel size, bit depth, exposure, channel, acquisition date) lives in the TIFF metadata, not the name.

Here is a small Python routine for checking a folder of TIFFs. It uses the tifffile library, which handles plain TIFF, OME-TIFF (a TIFF that stores standard microscopy metadata as XML) and most microscope vendor variants.

Install 

pip install tifffile
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Read one file 

import tifffile

path = "image_001.tif"
with tifffile.TiffFile(path) as tif:
    page = tif.pages[0]
    print("shape:", page.shape)
    print("dtype:", page.dtype)
    for tag in page.tags.values():
        print(tag.name, "=", tag.value)
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page.shape gives the pixel dimensions and page.dtype gives the bit depth. The difference between uint8 (whole numbers 0 to 255) and uint16 (0 to 65,535) matters a lot for intensity measurements. The loop prints every TIFF tag. The ones to look at first are XResolution, YResolution, ResolutionUnit and ImageDescription, because the pixel-to-micron calibration is usually in one of them.

OME-TIFF

If the file is OME-TIFF, the metadata is an XML block you can read directly:

with tifffile.TiffFile(path) as tif:
    if tif.is_ome:
        print(tif.ome_metadata)
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Check a whole folder 

from pathlib import Path
import tifffile

folder = Path("images")
for path in sorted(folder.glob("*.tif")):
    with tifffile.TiffFile(path) as tif:
        page = tif.pages[0]
        desc = page.tags.get("ImageDescription")
        print(path.name, page.shape, page.dtype, (desc.value[:60] if desc else ""))
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Run this once per experiment. If two images in the same set have different shapes, bit depths or calibration, you find out before you build a pipeline on them, not after.

Why it matters

Intensity-based measurements assume every image was acquired the same way. The metadata is the only record of whether that is true, so check it first.

More about my work: samdesmondschulman.com

Thanks for reading,

Sam

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