[ome-users] Bioformats gone!

[Curtis Rueden]

Hi Paul,

> Further to your update, I just started Fiji and was prompted to
> update. I did so, restarted and then discovered Bioformats had been
> completely removed!

There are a couple of bugs [1, 2] that might have caused this.

Please run Help > Update Fiji, click Advanced Mode. Click "Manage update
sites" and ensure that both "ImageJ" and "Fiji" are checked. ("Bio-Formats"
can be checked too if you want the Bio-Formats developer builds; that is up
to you.)

Next, click "Advanced mode" and change the View Options to "View
uninstalled files only". If you see any JARs there, especially anything
with "bio-formats" in the path, then mark it for installation (right-click
and "Install it"). Finally click "Apply changes" and then restart Fiji.

Please let us know if this does not fix the problem for you.

HTH,
Curtis

[1] https://github.com/imagej/imagej/issues/43
[2] https://github.com/imagej/imagej/issues/44


On Thu, Mar 6, 2014 at 7:24 AM, Paul Thomas (SCI) <P.Thomas at uea.ac.uk>wrote:

>  Hi Curtis,
>
>
>
> Further to your update, I just started Fiji and was prompted to update. I
> did so, restarted and then discovered Bioformats had been completely
> removed! I tried to update again; using "Manage sites" I checked
> Bioformats, but "Apply changes" is greyed-out so I cannot update to restore
> Bioformats.
>
>
>
> Fortunately, I have a back-up of my installation and can just copy the
> folder back, but there is clearly a problem here.
>
>
>
> Paul.
>
> ____________________
>
> Dr. Paul Thomas, Manager,
>
> The Henry Wellcome Laboratory for Cell Imaging,
>
> Faculty of Science,
>
> University of East Anglia,
>
> Norwich Research Park,
>
> Norwich,
>
> NR4 7TJ,
>
> United Kingdom.
>
>
>
> e-mail: p.thomas at uea.ac.uk
>
> Tel: +44-1603-592196
>
> Fax: +44-1603-592250
>
> Imaging web-site:
> https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab
>
> Personal web-page:
> https://www.uea.ac.uk/biological-sciences/research/facilities/henry-wellcome-lab/people
>
>
>
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