Matlab Toolbox not containing latest version of bioformats_package.jar?


I downloaded the Matlab Toolbox from Bio-Formats Downloads (OME), but when I ran bfUpgradeCheck I receive the following:

A new stable version of Bio-Formats is available


version = char(loci.formats.FormatTools.VERSION);

Returns version=5.1.2 rather than the expected 6.6.1 or equivalent.

Should Matlab’s jar be behind the current release? And if not, can the 6.6.1 Bio-Formats Package be switched out in the Matlab files?

I checked the newly-downloaded version because I was receiving a “Java Exception Error: Missing Library Java Advanced Imaging (JAI)”.

I tried to switch out bioformas_package.jar(6.6.1) and then received:

log4j:WARN No appenders could be found for logger (loci.formats.ClassList).
log4j:WARN Please initialize the log4j system properly.
ERROR: Java exception occurred:
loci.formats.FormatException: No IFDs found

I am running MATLAB 2021a and have Java 8 SE.
Any help greatly appreciated.

Hi @KE06, I double checked the latest version of the toolbox and the jar it contains is the correct 6.6.1 version. What looks to be happening is a conflict with a previous version which has been installed. If you run the command javaclasspath do you see any other versions of bioformas_package in a different location?

Hi @dgault my dynamic path returns a single instance of bioformats_package.jar in my current working folder. Static path returns the expected series.

As reference: I downloaded the Matlab Toolbox from the website, deleted my prior bioformats folder, and pasted in the freshly downloaded folder.

Within Matlab if you go to your current working folder, expand the bioformats_package.jar and look for the file META-INF/MANIFEST.MF and open it, you should see details as below. Does your jar show the version as 6.6.1 here?

Manifest-Version: 1.0
Main-Class: loci.formats.gui.ImageViewer
Implementation-Title: bioformats_package
Implementation-Version: 6.6.1
Implementation-Vendor-Id: ome
Implementation-Date: 23 March 2021
Implementation-Vendor: Open Microscopy Environment
Implementation-Build: a98d7261034f611ef0f33a54545476201341f978