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saalfeldlab / n5-spark

Spark-driven processing utilities for N5 datasets.
BSD 2-Clause "Simplified" License
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Converting bigtiff TIFF series fails #15

Open unidesigner opened 4 years ago

unidesigner commented 4 years ago

Hi, I'd like to convert a TIFF series to N5 using n5-spark, where the individual image sizes are large and I need to use bigtiff to store them (e.g. using the bigtiff parameter in scikit-image io). However, bigtiff do not seem to be supported, I get an Unsupported format or not found error, but it works fine for non-bigtiff images. How do you deal with converting large 2d image tiles to N5? Thanks!

igorpisarev commented 4 years ago

Hi @unidesigner, I haven't run into this problem since my TIFF slices were always less than 4 GB. I'm using simple ImageJ opener IJ.openImage() to read TIFF files which doesn't support bigtiff extensions. We could try a different opener such as BioFormats where bigtiff seems to be supported: https://docs.openmicroscopy.org/bio-formats/latest/formats/tiff.html I could look into it after the holidays, but PRs are welcome if you're willing to contribute!

unidesigner commented 4 years ago

Hi @igorpisarev - thanks for your quick reply. If it'd be easy for you to try the BioFormats opener after the holidays, that would be greatly appreciated. I'd probably take me too long to get into the java dev stack to just change this. Happy holidays!