[ome-users] Unable to open lif file

[Sebastien Besson (Staff)]

Dear Mai,

the fix for your LIF issue has been reviewed by the OME team and merged three days
ago into the development line (for reference the changes were finally handled in
https://github.com/openmicroscopy/bioformats/pull/1724).

This bug fix will be included in the next 5.1.1 release of Bio-Formats due by the end of this
month.

As you are using Fiji, the easiest way to retrieve the latest version of Bio-Formats including
this bug fix immediately is to enable the Bio-Formats update site following the instructions given
by Mark below (http://imagej.net/How_to_follow_a_3rd_party_update_site).

Best regards,
Sebastien

On 14 Apr 2015, at 13:11, Mark Hiner <hiner at wisc.edu<mailto:hiner at wisc.edu>> wrote:

Hi all,

>Can you briefly tell me what I need to do exactly in Fiji to be able to read my file with the solution.

>For Fiji, it's a bit more annoying because you first have to remove all the existing files related to bioformats before doing this.

Note that Roger's instructions only apply to testing Fiji/ImageJ with unmerged branches. Once https://github.com/openmicroscopy/bioformats/pull/1724 is merged, all you need to do is enable the Bio-Formats update site (http://imagej.net/How_to_follow_a_3rd_party_update_site) which is synchronized with the develop branch (https://github.com/openmicroscopy/bioformats). You would not need to manually modify any .jars, and should not need to wait for a 5.1.1 release to test this fix.

But note that even with this patch on the Bio-Formats update site, using a non-release version of Bio-Formats gives up reproducibility (http://imagej.net/Architecture#Reproducible_builds) and should only be used for testing - as Roger suggested.

Best,
Mark

On Tue, Apr 14, 2015 at 3:57 AM, Roger Leigh <rleigh at dundee.ac.uk<mailto:rleigh at dundee.ac.uk>> wrote:
On 13/04/15 19:54, Mai Tran wrote:
Hi Roger,

I'm new to using Fiji and coding. Can you briefly tell me what I need to
do exactly in Fiji to be able to read my file with the solution. My
guess is I need to append the provided code into my current Bioformat
plugins but I don't know how to access the Bioformat code in window8.

You can obtain the current build with this change merged in here:


https://ci.openmicroscopy.org/job/BIOFORMATS-5.1-merge-build/lastSuccessfulBuild/artifact/artifacts/

For plain ImageJ, you can use either loci_tools.jar or
bioformats_package.jar; just download and copy to the plugins directory
and restart ImageJ.
(http://www.openmicroscopy.org/site/support/bio-formats5.1/users/imagej/#upgrading)

For Fiji, it's a bit more annoying because you first have to remove all
the existing files related to bioformats before doing this.  See


https://github.com/bramalingam/bioformats/blob/Doc_Fiji_BFUpdate/docs/sphinx/users/fiji/index.txt

for some proposed instructions for doing this (it assumes the version is
5.0.7; just replace this with the version Fiji is currently using).

You might find it easier, for testing purposes, to use plain ImageJ
though.  When 5.1.1 is released, it should be updated in Fiji shortly after.



Kind regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096
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