[ome-users] Unable to open lif file

[Mark Hiner]

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> 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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>
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