Closed sbesson closed 2 years ago
This should be solved with the Bio-Formats 6.9.1 release which bumps cdm-core
to same version as the one used in jzarr
. This question of compatility matrix between the upstream Bio-Formats JARs and ZarrReader still remains but I think this is another component of the larger discussion in #32 so I am closing this issue in favor of the more recent one.
From the testing in https://github.com/ome/ZarrReader/pull/8
Using the latest Bio-Formats command-line tools bundle (6.9.1), extracting the OMEZarr artifact and executing it against sample data leads to
java.lang.NoSuchMethodError
when runningopenBytes
:Using the latest Bio-Formats 6.9.1-SNAPSHOT, including https://github.com/ome/bioformats/pull/3788 suffices to fix the error and display the data.
The alternative is to update https://github.com/ome/bioformats/blob/ef26436c2d079f05c1047816e564ffcc63bb0b04/tools/bf.sh#L60 and prepend the JAR to the classpath rather than appending it so that the latest
cdm-core
dependency is loaded first. In general though this is probably an incentive to moving towards a Bio-Formats (patch?) release with the cdm upgrade to make our tools less dependent on the classpath