Open Microscopy Environment

Hi all,

I'm using the latest version of bioformats (5.1.10) and I receive a strange warning message for the nd2 files I'm trying to read.

The following warning message is:

Java exception occurred:
Could not parse Temperature value: 0.3?TextInfoItem_TextInfoItem_TextInfoItem_912/08/2016 12:49:3TextInfoItem_1TextInfoItem_1TextInfoItem_1TextInfoItem_13Plan Apo ? 10x0R???t???..P


This warning is thrown in the last line of bfGerReader - r.setId(id) command

P.S.
Despite this warning, I'm still able to read the images and they look just fine... The thing is that I receive spammed emails full of these messages, which I also can't disable using warning('OFF') command in MATLAB.

Any help would be greatly appreciated.

Hi,

The warning('OFF') command in MATLAB will only affect MATLAB warnings but will not handle any output from Java. The warning that gets printed arises from the Bio-Formats logging system.

In Bio-Formats 5.1.10, you should be able to disable all Bio-Formats logging using the following command:

Code: Select all

loci.common.DebugTools.enableLogging('OFF');


In Bio-Formats 5.2.0 and above, you should use this command instead:

Code: Select all

loci.common.DebugTools.setRootLevel('OFF');


and information about setting the debugging level will be added to the Bio-Formats MATLAB documentation page

Best,
Sebastien

Hi, thanks

Bioformat 5.2.0 or above? The latest version I see is only 5.1.10

http://downloads.openmicroscopy.org/bio ... s/?C=M;O=D

where can I find 5.2.0 or above?
Thanks

Hi,

you are correct, the current stable and downloadable version of Bio-Formats is still 5.1.10.
We are actually working on the final release candidate of Bio-Formats 5.2.0 and expect to release it later this week. I mentioned it in my previous post to let you know that this particular API will change between 5.1 and 5.2 and might require some adaptation in your code if you start using it to silence Java warnings.

Best,
Sebastien