Stale ome-jai exclusion from ome-codecs breaks JPEG-2000 decoding (scifio dropped jai-imageio-jpeg2000 in 0.48.0)

[NicoKiaru]

Summary

pom-scijava excludes org.openmicroscopy:ome-jai from org.openmicroscopy:ome-codecs. The exclusion was correct when it was added in 43.0.0, but its premise expired with scifio 0.48.0. As a result, nothing on the classpath provides the com.sun.media.imageioimpl.plugins.jpeg2000.* classes that ome-codecs requires, and JPEG-2000 decoding is broken — in downstream builds and, since the 2026-07-16 update-site rebuild, in Fiji itself.

Symptom for end users: opening any JPEG-2000-compressed file (e.g. Olympus .vsi) fails with

The JAI Image I/O Tools are required to read JPEG-2000 files.

The stale premise

pom-scijava master, lines 4186-4195:

<dependency>
    <groupId>org.openmicroscopy</groupId>
    <artifactId>ome-codecs</artifactId>
    <version>${org.openmicroscopy.ome-codecs.version}</version>
    <exclusions>
        <exclusion>
            <!--
            Conflicts with com.github.jai-imageio:jai-imageio-jpeg2000,
            which io.scif:scifio depends on as of version 0.47.0.
            -->
            <groupId>org.openmicroscopy</groupId>
            <artifactId>ome-jai</artifactId>
        </exclusion>
    </exclusions>
</dependency>

io.scif:scifio no longer depends on com.github.jai-imageio:jai-imageio-jpeg2000. Checking the released poms:

scifio	depends on jai-imageio-jpeg2000?
0.45.0	no
0.46.0	no
0.47.0	yes (1.4.0) — the version the comment refers to
0.48.0	no — dependency removed again
0.49.0	no

And the corresponding pom-scijava versions:

pom-scijava	scifio.version	excludes ome-jai?
42.0.0	0.46.0	no
43.0.0	0.47.0	yes — correct at the time
44.0.0	0.48.0	yes — no longer correct
45.1.0	0.49.0	yes — no longer correct
45.1.1-SNAPSHOT (master)	0.49.0	yes — no longer correct

So from 44.0.0 onward the exclusion removes the only provider of the JPEG-2000 codec without anything taking its place.

Why scifio-jai-imageio does not cover it

io.scif:scifio-jai-imageio does ship a JJ2000 implementation, but under relocated package names (io.scif.jj2000.*, io.scif.media.*). ome-codecs' ome/codecs/services/JAIIIOServiceImpl hard-references the original coordinates:

com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageReader
com.sun.media.imageioimpl.plugins.jpeg2000.J2KImageWriter
com.sun.media.imageio.plugins.jpeg2000.J2KImageReadParam
com.sun.media.imageio.plugins.jpeg2000.J2KImageWriteParam

(from javap -c on ome-codecs 1.1.3)

The relocated classes therefore cannot satisfy it. Only ome-jai (and com.github.jai-imageio:jai-imageio-jpeg2000) provide com.sun.media.imageioimpl.plugins.jpeg2000.

Impact on Fiji

The Fiji update site was rebuilt on 2026-07-16 22:11:37, obsoleting 150 files. jars/ome-jai-0.1.5.jar is now recorded in https://sites.imagej.net/Fiji/db.xml.gz with no current <version> element — i.e. removed from the site:

<plugin filename="jars/ome-jai-0.1.5.jar">
    <previous-version timestamp="20250408132205" timestamp-obsolete="20250805105728" filename="jars/ome-jai-0.1.4.jar"/>
    <previous-version timestamp="20250805105727" timestamp-obsolete="20260716221137" filename="jars/ome-jai-0.1.5.jar"/>
</plugin>

This looks like a side effect of the exclusion rather than an intentional removal: of the 150 files obsoleted in that same upload, every other one was an ordinary version bump with a successor still on the site (imglib2-7.1.5 → 8.0.0, scijava-common-2.100.0 → 2.100.1, bigdataviewer-core-10.6.4 → 10.6.11, ...). ome-jai-0.1.5.jar is the only one with no replacement.

Meanwhile jars/ome-codecs-1.1.3.jar is still live on the site, so Fiji currently ships the codec front-end with no back-end. jai-imageio-jpeg2000 appears zero times in the site database, and jars/jai_imageio-1.0.1.jar and jars/jai-imageio-core-1.3.1.jar are themselves already obsoleted.

Scanning a current Fiji installation (666 jars in jars/) for the required class:

$ for j in *.jar; do unzip -l "$j" | grep -q "com/sun/media/imageioimpl/plugins/jpeg2000/J2KImageReader.class" && echo "PROVIDES: $j"; done
PROVIDES: ome-jai-0.1.5.jar

Exactly one provider, and the updater uninstalls it on every update. Marking it "keep installed" in the updater restores JPEG-2000 reading (it then shows as Obsolete), which confirms the missing class is the whole problem.

This affects all Fiji users reading JPEG-2000 data, not just one plugin.

Suggested fix

Either:

1. Drop the exclusion — since scifio 0.48.0 there is no longer a conflicting jai-imageio-jpeg2000 on the classpath, so ome-codecs can simply bring its own ome-jai again; or
2. Manage com.github.jai-imageio:jai-imageio-jpeg2000 explicitly in pom-scijava and keep the exclusion, if that implementation is preferred.

Option 1 restores the pre-43.0.0 behaviour with the smallest change. Whichever is chosen, ome-jai (or its replacement) will also need to be put back on the Fiji update site.

Environment

• pom-scijava 45.1.0 and 45.1.1-SNAPSHOT (master)
• scifio 0.49.0, ome-codecs 1.1.3, bio-formats 8.5.0
• Fiji (Fiji-Latest update site), Windows 11, Java 21

[imagesc-bot]

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

https://forum.image.sc/t/jpeg-2000-decompression-unsupported-in-fiji-latest/122413/3