Libjpeg-turbo exception when converting/opening .ndpi file.

[michaellee1]

Summary

I'm trying to convert an .ndpi file (Hamamatsu) to .tif, but the NDPI reader is throwing an error when I run conversion.

I've tried converting using:

1. bfconvert
2. python-bioformats bindings

to read in the image, and I'm getting the exact same error on both:

Exception

Exception in thread "main" java.lang.UnsatisfiedLinkError: 'void org.libjpegturbo.turbojpeg.TJDecompressor.init()'
	at org.libjpegturbo.turbojpeg.TJDecompressor.init(Native Method)
	at org.libjpegturbo.turbojpeg.TJDecompressor.<init>(TJDecompressor.java:81)
	at loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurboServiceImpl.java:346)
	at loci.formats.services.JPEGTurboServiceImpl.getTile(JPEGTurboServiceImpl.java:249)
	at loci.formats.in.NDPIReader.openBytes(NDPIReader.java:217)
	at loci.formats.FormatReader.openBytes(FormatReader.java:919)
	at loci.formats.ImageReader.openBytes(ImageReader.java:449)
	at loci.formats.tools.ImageConverter.getTile(ImageConverter.java:1085)
	at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:798)
	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:727)
	at loci.formats.tools.ImageConverter.main(ImageConverter.java:1126)

I'm actually able to open the image using FIJI's Bioformats plugin, but I'd like to do it programmatically. I'm stuck here on what can be done to convert these images using bioformats - is there a way to resolve this issue?

[petebankhead]

I am also unable to open .ndpi files because of libturbo issues if I am running on an ARM-based Mac and JDK intended for aarch64. However it works for me on the same Mac if I use a JDK intended for Intel processors.

Could this be the problem?

(Sorry for interjecting if not - I was meaning to report the Mac-specific behavior as it may soon become a blocker to releasing an apple-silicon-friendly version of QuPath.)

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/apple-m1-qupath/51637/8

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/omero-web-issues-with-fpbioimage-app-and-ndpi-files/78581/6

[imagesc-bot]

This issue has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/qupath-v0-4-3-fails-to-open-some-hamamatsu-ndpi-files-on-m1-mac/78887/2