Latest Bio-Formats in Fiji

[lechristophe]

Hi,

I'd like to know how to get the latest Bio-Formats (something like daily
builds) in Fiji. According to an email Curtis Rueden sent at the transition
between version 4 and 5 (
http://imagej.1557.x6.nabble.com/Fiji-s-Bio-Formats-will-be-updated-to-5-0-0-tp5006701p5006787.html),
checking the "Bio-Formats" update site should do that, or did I
misunderstood something? I checked the update site but it doesn't seem to
update Bio-Formats beyond the current Fiji version.

Thanks for your help,

Christophe

--
Christophe Leterrier
Researcher
Axonal Domains Architecture Team
CRN2M CNRS UMR 7286
Aix Marseille University, France

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner]

Hi Christophe,

>checking the "Bio-Formats" update site should do that, or did I
misunderstood something?

You understood perfectly. The Bio-Formats update site should give you the
latest Bio-Formats libraries.

>I checked the update site but it doesn't seem to update Bio-Formats beyond
the current Fiji version.

Can you clarify what behavior you're expecting? I just tested the update
site. The Wiki page <http://imagej.net/Bio-Formats#Daily_builds> mentioned
earlier in the thread you referenced also has instructions for checking the
version of your Bio-Formats - and mine went from 5.0.5 to 5.0.5-DEV, as
expected.

The 5.0.5 release was fairly recent, so I'm not sure what, if anything,
will be different on the daily build. Is there a specific fix you were
looking for that seems to be missing though?

Hope this helps,
Mark

On Wed, Oct 1, 2014 at 2:54 AM, Christophe Leterrier <
[hidden email]> wrote:

> Hi,
>
> I'd like to know how to get the latest Bio-Formats (something like daily
> builds) in Fiji. According to an email Curtis Rueden sent at the transition
> between version 4 and 5 (
>
> http://imagej.1557.x6.nabble.com/Fiji-s-Bio-Formats-will-be-updated-to-5-0-0-tp5006701p5006787.html
> ),
> checking the "Bio-Formats" update site should do that, or did I
> misunderstood something? I checked the update site but it doesn't seem to
> update Bio-Formats beyond the current Fiji version.
>
> Thanks for your help,
>
> Christophe
>
> --
> Christophe Leterrier
> Researcher
> Axonal Domains Architecture Team
> CRN2M CNRS UMR 7286
> Aix Marseille University, France
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[lechristophe]

Hi Mark,

I am indeed looking for a particular fix regarding large nd2 files:
https://github.com/openmicroscopy/bioformats/pull/1351

Melissa Linkert was kind enough to solve the problem and pointed me to get
it at:
http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/

I had some problem manually replacing files in Fiji's jar folder in the
past, so I'd have preferred to get it via the updater. As far as I
understand, the current dailies are 5.0, not 5.1 yet, which is where the
fix I'm looking for is right now?

Thanks for your help,

Christophe

2014-10-01 16:29 GMT+02:00 Mark Hiner <[hidden email]>:

> Hi Christophe,
>
> >checking the "Bio-Formats" update site should do that, or did I
> misunderstood something?
>
> You understood perfectly. The Bio-Formats update site should give you the
> latest Bio-Formats libraries.
>
> >I checked the update site but it doesn't seem to update Bio-Formats beyond
> the current Fiji version.
>
> Can you clarify what behavior you're expecting? I just tested the update
> site. The Wiki page <http://imagej.net/Bio-Formats#Daily_builds> mentioned
> earlier in the thread you referenced also has instructions for checking the
> version of your Bio-Formats - and mine went from 5.0.5 to 5.0.5-DEV, as
> expected.
>
> The 5.0.5 release was fairly recent, so I'm not sure what, if anything,
> will be different on the daily build. Is there a specific fix you were
> looking for that seems to be missing though?
>
> Hope this helps,
> Mark
>
> On Wed, Oct 1, 2014 at 2:54 AM, Christophe Leterrier <
> [hidden email]> wrote:
>
> > Hi,
> >
> > I'd like to know how to get the latest Bio-Formats (something like daily
> > builds) in Fiji. According to an email Curtis Rueden sent at the
> transition
> > between version 4 and 5 (
> >
> >
> http://imagej.1557.x6.nabble.com/Fiji-s-Bio-Formats-will-be-updated-to-5-0-0-tp5006701p5006787.html
> > ),
> > checking the "Bio-Formats" update site should do that, or did I
> > misunderstood something? I checked the update site but it doesn't seem to
> > update Bio-Formats beyond the current Fiji version.
> >
> > Thanks for your help,
> >
> > Christophe
> >
> > --
> > Christophe Leterrier
> > Researcher
> > Axonal Domains Architecture Team
> > CRN2M CNRS UMR 7286
> > Aix Marseille University, France
> >
> > --
> > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 10/1/14, 6:44 PM, Christophe Leterrier wrote:

> Hi Mark,
>
> I am indeed looking for a particular fix regarding large nd2 files:
> https://github.com/openmicroscopy/bioformats/pull/1351
>
> Melissa Linkert was kind enough to solve the problem and pointed me to get
> it at:
> http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
>
> I had some problem manually replacing files in Fiji's jar folder in the
> past, so I'd have preferred to get it via the updater. As far as I
> understand, the current dailies are 5.0, not 5.1 yet, which is where the
> fix I'm looking for is right now?

This may be similar to the bug #12548 on the OME list.

I tried the version pointed by the above link. It has the same problem
as the latest update found by the updater.
In each case, using the 5.0.2 version of the formats-gpl.jar file solves
the problem (at least for my large nd2 files)


--aryeh

> Thanks for your help,
>
> Christophe
>
> 2014-10-01 16:29 GMT+02:00 Mark Hiner <[hidden email]>:
>
>> Hi Christophe,
>>
>>> checking the "Bio-Formats" update site should do that, or did I
>> misunderstood something?
>>
>> You understood perfectly. The Bio-Formats update site should give you the
>> latest Bio-Formats libraries.
>>
>>> I checked the update site but it doesn't seem to update Bio-Formats beyond
>> the current Fiji version.
>>
>> Can you clarify what behavior you're expecting? I just tested the update
>> site. The Wiki page <http://imagej.net/Bio-Formats#Daily_builds> mentioned
>> earlier in the thread you referenced also has instructions for checking the
>> version of your Bio-Formats - and mine went from 5.0.5 to 5.0.5-DEV, as
>> expected.
>>
>> The 5.0.5 release was fairly recent, so I'm not sure what, if anything,
>> will be different on the daily build. Is there a specific fix you were
>> looking for that seems to be missing though?
>>
>> Hope this helps,
>> Mark
>>
>> On Wed, Oct 1, 2014 at 2:54 AM, Christophe Leterrier <
>> [hidden email]> wrote:
>>
>>> Hi,
>>>
>>> I'd like to know how to get the latest Bio-Formats (something like daily
>>> builds) in Fiji. According to an email Curtis Rueden sent at the
>> transition
>>> between version 4 and 5 (
>>>
>>>
>> http://imagej.1557.x6.nabble.com/Fiji-s-Bio-Formats-will-be-updated-to-5-0-0-tp5006701p5006787.html
>>> ),
>>> checking the "Bio-Formats" update site should do that, or did I
>>> misunderstood something? I checked the update site but it doesn't seem to
>>> update Bio-Formats beyond the current Fiji version.
>>>
>>> Thanks for your help,
>>>
>>> Christophe
>>>
>>> --
>>> Christophe Leterrier
>>> Researcher
>>> Axonal Domains Architecture Team
>>> CRN2M CNRS UMR 7286
>>> Aix Marseille University, France
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner]

Hi Christophe,

>As far as I understand, the current dailies are 5.0, not 5.1 yet

You are correct. We will be switching over to 5.1.x, but in the mean time
it looks like the nd2 fix
<https://github.com/openmicroscopy/bioformats/commit/3c857c2e5743e9b23801408bd61de49697716b4d>
you're looking for only affected the formats-gpl component. You should be
able to just download that specific jar, and replace the
formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
version will just be called "formats-gpl.jar" if you still have the
Bio-Formats update site enabled).

I hope that will hold you over until we migrate to the 5.1.x daily builds,
but please let us know if there are any problems manually replacing the jar.

Thanks,
Mark

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[lechristophe]

Hi Mark,

Thanks for the advice; I tried to replace the formats-gpl.jar in the
jars/bioformats directory (daily build) with the version currently on
Jenkins for 5.1. After that I tried to open the big nd2 file I uploaded to
people at Bio-Formats. After half a minute with no big memory usage (around
70 MB), I get a new error:

(Fiji Is Just) ImageJ 2.0.0-rc-14/1.49g; Java 1.6.0_24 [64-bit]; Windows 7
6.1; 61MB of 49071MB (<1%)

java.lang.NoSuchMethodError:
loci.formats.FormatTools.getEmissionWavelength(Ljava/lang/Double;)Lome/xml/model/primitives/PositiveFloat;
at
loci.formats.in.NativeND2Reader.populateMetadataStore(NativeND2Reader.java:1928)
at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1316)
at loci.formats.FormatReader.setId(FormatReader.java:1317)
at loci.formats.DelegateReader.setId(DelegateReader.java:253)
at loci.formats.ImageReader.setId(ImageReader.java:753)
at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388)
at io.scif.AbstractParser.parse(AbstractParser.java:252)
at io.scif.AbstractParser.parse(AbstractParser.java:335)
at io.scif.AbstractParser.parse(AbstractParser.java:52)
at io.scif.AbstractReader.setSource(AbstractReader.java:270)
at
io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
at
net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
at
net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
at
net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)
at ij.IJ.runPlugIn(IJ.java)
at ij.Executer.runCommand(Executer.java:131)
at ij.Executer.run(Executer.java:64)
at java.lang.Thread.run(Thread.java:662)

so I guess something else was modified in the new jar that keeps him from
playing nice with the rest of the daily build?

Christophe



2014-10-01 21:21 GMT+02:00 Mark Hiner <[hidden email]>:

> Hi Christophe,
>
> >As far as I understand, the current dailies are 5.0, not 5.1 yet
>
> You are correct. We will be switching over to 5.1.x, but in the mean time
> it looks like the nd2 fix
> <https://github.com/openmicroscopy/bioformats/commit/3c857c2e5743e9b23801408bd61de49697716b4d>
> you're looking for only affected the formats-gpl component. You should be
> able to just download that specific jar, and replace the
> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
> version will just be called "formats-gpl.jar" if you still have the
> Bio-Formats update site enabled).
>
> I hope that will hold you over until we migrate to the 5.1.x daily builds,
> but please let us know if there are any problems manually replacing the jar.
>
> Thanks,
> Mark
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner]

Hi Christophe,

>so I guess something else was modified in the new jar that keeps him from
playing nice with the rest of the daily build?

Sort of; the "NoSuchMethodError" means that the ND2Reader is using API
("getEmissionWavelength" method) that doesn't exist in the version (5.0.x)
of your FormatTools class it has access to. This means that it needs the
5.1.x FormatTools class.

So at this point you could either:

a) download all the 5.1.x jars from Jenkins and switch to these. I assume
there will be new dependency jars you'll end up having to track down.

or

b) Continue to download and replace just the components are needed, using
the same process you did with formats-gpl. FormatTools is in the
"formats-api" jar. If you keep getting "NoSuchMethodError"s, you can look
up the class with the missing method on the Bio-Formats GitHub
<https://github.com/openmicroscopy/bioformats/find/develop>. For example, I
saw that FormatTools.java is in /components/formats-api, so I knew you
needed the formats-api.jar.

You can of course also wait for us to set the update site to 5.1.x, but
these are your fastest options.

Hope this helps. Please let me know if you have any other problems or
questions.

Regards,
Mark



On Fri, Oct 3, 2014 at 7:16 AM, Christophe Leterrier <
[hidden email]> wrote:

> Hi Mark,
>
> Thanks for the advice; I tried to replace the formats-gpl.jar in the
> jars/bioformats directory (daily build) with the version currently on
> Jenkins for 5.1. After that I tried to open the big nd2 file I uploaded to
> people at Bio-Formats. After half a minute with no big memory usage (around
> 70 MB), I get a new error:
>
> (Fiji Is Just) ImageJ 2.0.0-rc-14/1.49g; Java 1.6.0_24 [64-bit]; Windows 7
> 6.1; 61MB of 49071MB (<1%)
>
> java.lang.NoSuchMethodError:
> loci.formats.FormatTools.getEmissionWavelength(Ljava/lang/Double;)Lome/xml/model/primitives/PositiveFloat;
> at
> loci.formats.in.NativeND2Reader.populateMetadataStore(NativeND2Reader.java:1928)
> at loci.formats.in.NativeND2Reader.initFile(NativeND2Reader.java:1316)
> at loci.formats.FormatReader.setId(FormatReader.java:1317)
> at loci.formats.DelegateReader.setId(DelegateReader.java:253)
> at loci.formats.ImageReader.setId(ImageReader.java:753)
> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:388)
> at io.scif.AbstractParser.parse(AbstractParser.java:252)
> at io.scif.AbstractParser.parse(AbstractParser.java:335)
> at io.scif.AbstractParser.parse(AbstractParser.java:52)
> at io.scif.AbstractReader.setSource(AbstractReader.java:270)
> at
> io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
> at io.scif.img.ImgOpener.createReader(ImgOpener.java:542)
> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:144)
> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:266)
> at net.imagej.DefaultDatasetService.open(DefaultDatasetService.java:250)
> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:78)
> at net.imagej.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
> at
> net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:134)
> at
> net.imagej.legacy.DefaultLegacyHooks.interceptFileOpen(DefaultLegacyHooks.java:327)
> at
> net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:150)
> at ij.IJ.runPlugIn(IJ.java)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:662)
>
> so I guess something else was modified in the new jar that keeps him from
> playing nice with the rest of the daily build?
>
> Christophe
>
>
>
> 2014-10-01 21:21 GMT+02:00 Mark Hiner <[hidden email]>:
>
>> Hi Christophe,
>>
>> >As far as I understand, the current dailies are 5.0, not 5.1 yet
>>
>> You are correct. We will be switching over to 5.1.x, but in the mean time
>> it looks like the nd2 fix
>> <https://github.com/openmicroscopy/bioformats/commit/3c857c2e5743e9b23801408bd61de49697716b4d>
>> you're looking for only affected the formats-gpl component. You should be
>> able to just download that specific jar, and replace the
>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
>> version will just be called "formats-gpl.jar" if you still have the
>> Bio-Formats update site enabled).
>>
>> I hope that will hold you over until we migrate to the 5.1.x daily
>> builds, but please let us know if there are any problems manually replacing
>> the jar.
>>
>> Thanks,
>> Mark
>>
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner]

Hi Aryeh,

>How can I turn this into the formats-gpl.jar file?

Great question! I'm cc'ing the list because I think this information is of
general interest.

The Bio-Formats site has a page with instructions for downloading and
building the jars from source:
https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html

After cloning the Bio-Formats repository
<http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
you can either:
* Check out a specific tag
<http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
or
* Check out a specific commit
<http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>

Or it should be fine to just build the "develop" branch, since the patch in
question was merged.

After building Bio-Formats, all the output .jars will be in the /artifacts
sub-directory of your Bio-Formats checkout.

Let me know if you have any more questions, and thank you for taking the
time to test this!

Regards,
Mark


On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss <[hidden email]> wrote:

> Hi Mark
>
> On 10/1/14, 10:21 PM, Mark Hiner wrote:
>
>> Hi Christophe,
>>
>>  As far as I understand, the current dailies are 5.0, not 5.1 yet
>>>
>> You are correct. We will be switching over to 5.1.x, but in the mean time
>> it looks like the nd2 fix
>> <https://github.com/openmicroscopy/bioformats/commit/
>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>> you're looking for only affected the formats-gpl component. You should be
>> able to just download that specific jar, and replace the
>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
>> version will just be called "formats-gpl.jar" if you still have the
>> Bio-Formats update site enabled).
>>
>
> How can I turn this into the formats-gpl.jar file?
> If I can do that, I will replace my version 5.0.2 file, and see if it
> works properly
>
> thanks and best regards
> --aryeh
>
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Melissa Linkert-2]

Hi Aryeh,

> >> You are correct. We will be switching over to 5.1.x, but in the mean time
> >> it looks like the nd2 fix
> >> <https://github.com/openmicroscopy/bioformats/commit/
> >> 3c857c2e5743e9b23801408bd61de49697716b4d>
> >> you're looking for only affected the formats-gpl component. You should be
> >> able to just download that specific jar, and replace the
> >> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
> >> version will just be called "formats-gpl.jar" if you still have the
> >> Bio-Formats update site enabled).
> >>
> >
> > How can I turn this into the formats-gpl.jar file?
> > If I can do that, I will replace my version 5.0.2 file, and see if it
> > works properly

Instead of compiling from source, you can also download the latest 5.1
builds from:

http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/

For anyone trying this though, please do note that mixing 5.1 and 5.0
files is not supported and very unlikely to work, so you will need to
update all files to 5.1.  Be aware that this can cause problems with
other plugins that use Bio-Formats, as there are API differences between
the two versions (though we have not yet released 5.1.0).

We are also considering this fix for a 5.0.6 release of Bio-Formats, which
would eliminate the need to manually update files.

Regards,
-Melissa

On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:

> Hi Aryeh,
>
> >How can I turn this into the formats-gpl.jar file?
>
> Great question! I'm cc'ing the list because I think this information is of
> general interest.
>
> The Bio-Formats site has a page with instructions for downloading and
> building the jars from source:
> https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html
>
> After cloning the Bio-Formats repository
> <http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
> you can either:
> * Check out a specific tag
> <http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
> or
> * Check out a specific commit
> <http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>
> Or it should be fine to just build the "develop" branch, since the patch in
> question was merged.
>
> After building Bio-Formats, all the output .jars will be in the /artifacts
> sub-directory of your Bio-Formats checkout.
>
> Let me know if you have any more questions, and thank you for taking the
> time to test this!
>
> Regards,
> Mark
>
>
> On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss <[hidden email]> wrote:
>
> > Hi Mark
> >
> > On 10/1/14, 10:21 PM, Mark Hiner wrote:
> >
> >> Hi Christophe,
> >>
> >>  As far as I understand, the current dailies are 5.0, not 5.1 yet
> >>>
> >> You are correct. We will be switching over to 5.1.x, but in the mean time
> >> it looks like the nd2 fix
> >> <https://github.com/openmicroscopy/bioformats/commit/
> >> 3c857c2e5743e9b23801408bd61de49697716b4d>
> >> you're looking for only affected the formats-gpl component. You should be
> >> able to just download that specific jar, and replace the
> >> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
> >> version will just be called "formats-gpl.jar" if you still have the
> >> Bio-Formats update site enabled).
> >>
> >
> > How can I turn this into the formats-gpl.jar file?
> > If I can do that, I will replace my version 5.0.2 file, and see if it
> > works properly
> >
> > thanks and best regards
> > --aryeh
> >
> >
> > --
> > Aryeh Weiss
> > Faculty of Engineering
> > Bar Ilan University
> > Ramat Gan 52900 Israel
> >
> > Ph:  972-3-5317638
> > FAX: [phone]
> >
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Hi Melissa

On 10/6/14, 4:27 PM, Melissa Linkert wrote:

> Hi Aryeh,
>
>>>> You are correct. We will be switching over to 5.1.x, but in the mean time
>>>> it looks like the nd2 fix
>>>> <https://github.com/openmicroscopy/bioformats/commit/
>>>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>>>> you're looking for only affected the formats-gpl component. You should be
>>>> able to just download that specific jar, and replace the
>>>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
>>>> version will just be called "formats-gpl.jar" if you still have the
>>>> Bio-Formats update site enabled).
>>>>
>>> How can I turn this into the formats-gpl.jar file?
>>> If I can do that, I will replace my version 5.0.2 file, and see if it
>>> works properly
> Instead of compiling from source, you can also download the latest 5.1
> builds from:
>
> http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
>
> For anyone trying this though, please do note that mixing 5.1 and 5.0
> files is not supported and very unlikely to work, so you will need to
> update all files to 5.1.  Be aware that this can cause problems with
> other plugins that use Bio-Formats, as there are API differences between
> the two versions (though we have not yet released 5.1.0).

Thank you (and also Mark) for your replies.
I downloaded the  5.1 builds for all of the jar files in the
jars/bio-formats directory of my Fiji distribution.
When I dragged one of my nd2 files into Fiji, bio-formats opened, but
had the same bug as reported previously.
When I restored the old bio-formats directory with the 5.0.2 version of
gpl, it worked properly.
I did not try the 5.0.2 gpl with the 5.1 release, because of Melissa
warning concerning mixing the two versions.


Best regards
--aryeh

> We are also considering this fix for a 5.0.6 release of Bio-Formats, which
> would eliminate the need to manually update files.
>
> Regards,
> -Melissa
>
> On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
>> Hi Aryeh,
>>
>>> How can I turn this into the formats-gpl.jar file?
>> Great question! I'm cc'ing the list because I think this information is of
>> general interest.
>>
>> The Bio-Formats site has a page with instructions for downloading and
>> building the jars from source:
>> https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html
>>
>> After cloning the Bio-Formats repository
>> <http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
>> you can either:
>> * Check out a specific tag
>> <http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
>> or
>> * Check out a specific commit
>> <http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>>
>> Or it should be fine to just build the "develop" branch, since the patch in
>> question was merged.
>>
>> After building Bio-Formats, all the output .jars will be in the /artifacts
>> sub-directory of your Bio-Formats checkout.
>>
>> Let me know if you have any more questions, and thank you for taking the
>> time to test this!
>>
>> Regards,
>> Mark
>>
>>
>> On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss <[hidden email]> wrote:
>>
>>> Hi Mark
>>>
>>> On 10/1/14, 10:21 PM, Mark Hiner wrote:
>>>
>>>> Hi Christophe,
>>>>
>>>>   As far as I understand, the current dailies are 5.0, not 5.1 yet
>>>> You are correct. We will be switching over to 5.1.x, but in the mean time
>>>> it looks like the nd2 fix
>>>> <https://github.com/openmicroscopy/bioformats/commit/
>>>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>>>> you're looking for only affected the formats-gpl component. You should be
>>>> able to just download that specific jar, and replace the
>>>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the old
>>>> version will just be called "formats-gpl.jar" if you still have the
>>>> Bio-Formats update site enabled).
>>>>
>>> How can I turn this into the formats-gpl.jar file?
>>> If I can do that, I will replace my version 5.0.2 file, and see if it
>>> works properly
>>>
>>> thanks and best regards
>>> --aryeh
>>>
>>>
>>>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 10/6/14, 11:17 PM, Aryeh Weiss wrote:

> Hi Melissa
>
> On 10/6/14, 4:27 PM, Melissa Linkert wrote:
>> Hi Aryeh,
>>
>>>>> You are correct. We will be switching over to 5.1.x, but in the
>>>>> mean time
>>>>> it looks like the nd2 fix
>>>>> <https://github.com/openmicroscopy/bioformats/commit/
>>>>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>>>>> you're looking for only affected the formats-gpl component. You
>>>>> should be
>>>>> able to just download that specific jar, and replace the
>>>>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory
>>>>> (the old
>>>>> version will just be called "formats-gpl.jar" if you still have the
>>>>> Bio-Formats update site enabled).
>>>>>
>>>> How can I turn this into the formats-gpl.jar file?
>>>> If I can do that, I will replace my version 5.0.2 file, and see if it
>>>> works properly
>> Instead of compiling from source, you can also download the latest 5.1
>> builds from:
>>
>> http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/ 
>>
>>
>> For anyone trying this though, please do note that mixing 5.1 and 5.0
>> files is not supported and very unlikely to work, so you will need to
>> update all files to 5.1.  Be aware that this can cause problems with
>> other plugins that use Bio-Formats, as there are API differences between
>> the two versions (though we have not yet released 5.1.0).
>
> Thank you (and also Mark) for your replies.
> I downloaded the  5.1 builds for all of the jar files in the
> jars/bio-formats directory of my Fiji distribution.
> When I dragged one of my nd2 files into Fiji, bio-formats opened, but
> had the same bug as reported previously.
> When I restored the old bio-formats directory with the 5.0.2 version
> of gpl, it worked properly.
> I did not try the 5.0.2 gpl with the 5.1 release, because of Melissa
> warning concerning mixing the two versions.
>
>
> Best regards
> --aryeh
>
>
>> We are also considering this fix for a 5.0.6 release of Bio-Formats,
>> which
>> would eliminate the need to manually update files.
>>
>> Regards,
>> -Melissa
>>

About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
updater to update formats-gpl.
The updated version correctly read my multifield ND2, so I thought that
this bug was resolved.
However, yesterday, following an update, the problem reappeared.
Again,the workaround was to use the 5.0.2 version of
formats-gpl.

I have not had a chance to search my recent backups for this file to see
if I can determine exactly when it broke again -- I will try to do that.


Best regards,
--aryeh

>> On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
>>> Hi Aryeh,
>>>
>>>> How can I turn this into the formats-gpl.jar file?
>>> Great question! I'm cc'ing the list because I think this information
>>> is of
>>> general interest.
>>>
>>> The Bio-Formats site has a page with instructions for downloading and
>>> building the jars from source:
>>> https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html 
>>>
>>>
>>> After cloning the Bio-Formats repository
>>> <http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
>>>
>>> you can either:
>>> * Check out a specific tag
>>> <http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
>>>
>>> or
>>> * Check out a specific commit
>>> <http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>>>
>>>
>>> Or it should be fine to just build the "develop" branch, since the
>>> patch in
>>> question was merged.
>>>
>>> After building Bio-Formats, all the output .jars will be in the
>>> /artifacts
>>> sub-directory of your Bio-Formats checkout.
>>>
>>> Let me know if you have any more questions, and thank you for taking
>>> the
>>> time to test this!
>>>
>>> Regards,
>>> Mark
>>>
>>>
>>> On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss <[hidden email]>
>>> wrote:
>>>
>>>> Hi Mark
>>>>
>>>> On 10/1/14, 10:21 PM, Mark Hiner wrote:
>>>>
>>>>> Hi Christophe,
>>>>>
>>>>>   As far as I understand, the current dailies are 5.0, not 5.1 yet
>>>>> You are correct. We will be switching over to 5.1.x, but in the
>>>>> mean time
>>>>> it looks like the nd2 fix
>>>>> <https://github.com/openmicroscopy/bioformats/commit/
>>>>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>>>>> you're looking for only affected the formats-gpl component. You
>>>>> should be
>>>>> able to just download that specific jar, and replace the
>>>>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory
>>>>> (the old
>>>>> version will just be called "formats-gpl.jar" if you still have the
>>>>> Bio-Formats update site enabled).
>>>>>
>>>> How can I turn this into the formats-gpl.jar file?
>>>> If I can do that, I will replace my version 5.0.2 file, and see if it
>>>> works properly
>>>>
>>>> thanks and best regards
>>>> --aryeh
>>>>
>>>>
>>>>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Aryeh,

> About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
> updater to update formats-gpl. The updated version correctly read my
> multifield ND2, so I thought that this bug was resolved. However,
> yesterday, following an update, the problem reappeared. Again,the
> workaround was to use the 5.0.2 version of formats-gpl.

That is very odd. It would be great if you could somehow isolate the
difference between the working version of Fiji vs. the non-working
one—especially if they both used Bio-Formats 5.0.6.

What happens if you enable the Bio-Formats update site? Still non-working?

If you get a chance, you could also test with the "showinf" command line
tool [1], which would rule out any Fiji-specific installation issues. And
of course testing from multiple different machines might also shed some
light on things.

Regards,
Curtis

[1] http://openmicroscopy.org/site/support/bio-formats5/users/comlinetools/

On Thu, Nov 27, 2014 at 1:45 AM, Aryeh Weiss <[hidden email]> wrote:

> On 10/6/14, 11:17 PM, Aryeh Weiss wrote:
>
>> Hi Melissa
>>
>> On 10/6/14, 4:27 PM, Melissa Linkert wrote:
>>
>>> Hi Aryeh,
>>>
>>>  You are correct. We will be switching over to 5.1.x, but in the mean
>>>>>> time
>>>>>> it looks like the nd2 fix
>>>>>> <https://github.com/openmicroscopy/bioformats/commit/
>>>>>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>>>>>> you're looking for only affected the formats-gpl component. You
>>>>>> should be
>>>>>> able to just download that specific jar, and replace the
>>>>>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the
>>>>>> old
>>>>>> version will just be called "formats-gpl.jar" if you still have the
>>>>>> Bio-Formats update site enabled).
>>>>>>
>>>>>>  How can I turn this into the formats-gpl.jar file?
>>>>> If I can do that, I will replace my version 5.0.2 file, and see if it
>>>>> works properly
>>>>>
>>>> Instead of compiling from source, you can also download the latest 5.1
>>> builds from:
>>>
>>> http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/
>>> lastSuccessfulBuild/artifact/artifacts/
>>>
>>> For anyone trying this though, please do note that mixing 5.1 and 5.0
>>> files is not supported and very unlikely to work, so you will need to
>>> update all files to 5.1.  Be aware that this can cause problems with
>>> other plugins that use Bio-Formats, as there are API differences between
>>> the two versions (though we have not yet released 5.1.0).
>>>
>>
>> Thank you (and also Mark) for your replies.
>> I downloaded the  5.1 builds for all of the jar files in the
>> jars/bio-formats directory of my Fiji distribution.
>> When I dragged one of my nd2 files into Fiji, bio-formats opened, but had
>> the same bug as reported previously.
>> When I restored the old bio-formats directory with the 5.0.2 version of
>> gpl, it worked properly.
>> I did not try the 5.0.2 gpl with the 5.1 release, because of Melissa
>> warning concerning mixing the two versions.
>>
>>
>> Best regards
>> --aryeh
>>
>>
>>  We are also considering this fix for a 5.0.6 release of Bio-Formats,
>>> which
>>> would eliminate the need to manually update files.
>>>
>>> Regards,
>>> -Melissa
>>>
>>>
> About two weeks ago, when 5.0.6 was announced, I allowed the Fiji updater
> to update formats-gpl.
> The updated version correctly read my multifield ND2, so I thought that
> this bug was resolved.
> However, yesterday, following an update, the problem reappeared. Again,the
> workaround was to use the 5.0.2 version of
> formats-gpl.
>
> I have not had a chance to search my recent backups for this file to see
> if I can determine exactly when it broke again -- I will try to do that.
>
>
> Best regards,
> --aryeh
>
>
>
>  On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
>>>
>>>> Hi Aryeh,
>>>>
>>>>  How can I turn this into the formats-gpl.jar file?
>>>>>
>>>> Great question! I'm cc'ing the list because I think this information is
>>>> of
>>>> general interest.
>>>>
>>>> The Bio-Formats site has a page with instructions for downloading and
>>>> building the jars from source:
>>>> https://www.openmicroscopy.org/site/support/bio-formats5/
>>>> developers/building-bioformats.html
>>>>
>>>> After cloning the Bio-Formats repository
>>>> <http://git-scm.com/book/en/Git-Basics-Getting-a-Git-
>>>> Repository#Cloning-an-Existing-Repository>,
>>>> you can either:
>>>> * Check out a specific tag
>>>> <http://stackoverflow.com/questions/791959/download-a-
>>>> specific-tag-with-git>
>>>> or
>>>> * Check out a specific commit
>>>> <http://stackoverflow.com/questions/2007662/rollback-to-
>>>> an-old-commit-using-git>
>>>>
>>>> Or it should be fine to just build the "develop" branch, since the
>>>> patch in
>>>> question was merged.
>>>>
>>>> After building Bio-Formats, all the output .jars will be in the
>>>> /artifacts
>>>> sub-directory of your Bio-Formats checkout.
>>>>
>>>> Let me know if you have any more questions, and thank you for taking the
>>>> time to test this!
>>>>
>>>> Regards,
>>>> Mark
>>>>
>>>>
>>>> On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss <[hidden email]>
>>>> wrote:
>>>>
>>>>  Hi Mark
>>>>>
>>>>> On 10/1/14, 10:21 PM, Mark Hiner wrote:
>>>>>
>>>>>  Hi Christophe,
>>>>>>
>>>>>>   As far as I understand, the current dailies are 5.0, not 5.1 yet
>>>>>> You are correct. We will be switching over to 5.1.x, but in the mean
>>>>>> time
>>>>>> it looks like the nd2 fix
>>>>>> <https://github.com/openmicroscopy/bioformats/commit/
>>>>>> 3c857c2e5743e9b23801408bd61de49697716b4d>
>>>>>> you're looking for only affected the formats-gpl component. You
>>>>>> should be
>>>>>> able to just download that specific jar, and replace the
>>>>>> formats-gpl-5.0.5.jar in your Fiji.app/jars/bioformats directory (the
>>>>>> old
>>>>>> version will just be called "formats-gpl.jar" if you still have the
>>>>>> Bio-Formats update site enabled).
>>>>>>
>>>>>>  How can I turn this into the formats-gpl.jar file?
>>>>> If I can do that, I will replace my version 5.0.2 file, and see if it
>>>>> works properly
>>>>>
>>>>> thanks and best regards
>>>>> --aryeh
>>>>>
>>>>>
>>>>>
>>>>>
>>
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 12/6/14, 12:16 AM, Curtis Rueden wrote:

> Hi Aryeh,
>
> > About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
> > updater to update formats-gpl. The updated version correctly read my
> > multifield ND2, so I thought that this bug was resolved. However,
> > yesterday, following an update, the problem reappeared. Again,the
> > workaround was to use the 5.0.2 version of formats-gpl.
>
> That is very odd. It would be great if you could somehow isolate the
> difference between the working version of Fiji vs. the non-working
> one—especially if they both used Bio-Formats 5.0.6.
>

I checked my backups, and I have been unable to find a working updated
bioformats-gpl in my recent backups. This most likely means that I was
mistaken about the problem being temporarily fixed.
> What happens if you enable the Bio-Formats update site? Still non-working?
>
It fails both ways.
Here is the info form teh advanced mode of the updater for the two
bioformats-gpl files:

bioformats from fiji site
bioformats-gpl-5.0.6
Modified 11 Nov 2014

bioformats from bioformats site
bioformats-gpl
Modified 04 Nov 2014

Both fail the same way.
> If you get a chance, you could also test with the "showinf" command
> line tool [1], which would rule out any Fiji-specific installation
> issues. And of course testing from multiple different machines might
> also shed some light on things.
>
The showinf output has the same error -- it is not Fiji specific.
I can also tell you that the same problem occurs on a Windows 7-64bit
OS, and the workaroudn is identical (fall back to gpl-5.0.2

As long as the workaround works, it is ok. However, that seems like
living on borrowed time...
> Regards,
> Curtis
>
Thank you for your attention to this.

Best regards,
--aryeh

> [1]
> http://openmicroscopy.org/site/support/bio-formats5/users/comlinetools/
>
> On Thu, Nov 27, 2014 at 1:45 AM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     On 10/6/14, 11:17 PM, Aryeh Weiss wrote:
>
>         Hi Melissa
>
>         On 10/6/14, 4:27 PM, Melissa Linkert wrote:
>
>             Hi Aryeh,
>
>                         You are correct. We will be switching over to
>                         5.1.x, but in the mean time
>                         it looks like the nd2 fix
>                         <https://github.com/openmicroscopy/bioformats/commit/
>                         3c857c2e5743e9b23801408bd61de49697716b4d>
>                         you're looking for only affected the
>                         formats-gpl component. You should be
>                         able to just download that specific jar, and
>                         replace the
>                         formats-gpl-5.0.5.jar in your
>                         Fiji.app/jars/bioformats directory (the old
>                         version will just be called "formats-gpl.jar"
>                         if you still have the
>                         Bio-Formats update site enabled).
>
>                     How can I turn this into the formats-gpl.jar file?
>                     If I can do that, I will replace my version 5.0.2
>                     file, and see if it
>                     works properly
>
>             Instead of compiling from source, you can also download
>             the latest 5.1
>             builds from:
>
>             http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
>
>
>             For anyone trying this though, please do note that mixing
>             5.1 and 5.0
>             files is not supported and very unlikely to work, so you
>             will need to
>             update all files to 5.1.  Be aware that this can cause
>             problems with
>             other plugins that use Bio-Formats, as there are API
>             differences between
>             the two versions (though we have not yet released 5.1.0).
>
>
>         Thank you (and also Mark) for your replies.
>         I downloaded the  5.1 builds for all of the jar files in the
>         jars/bio-formats directory of my Fiji distribution.
>         When I dragged one of my nd2 files into Fiji, bio-formats
>         opened, but had the same bug as reported previously.
>         When I restored the old bio-formats directory with the 5.0.2
>         version of gpl, it worked properly.
>         I did not try the 5.0.2 gpl with the 5.1 release, because of
>         Melissa warning concerning mixing the two versions.
>
>
>         Best regards
>         --aryeh
>
>
>             We are also considering this fix for a 5.0.6 release of
>             Bio-Formats, which
>             would eliminate the need to manually update files.
>
>             Regards,
>             -Melissa
>
>
>     About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
>     updater to update formats-gpl.
>     The updated version correctly read my multifield ND2, so I thought
>     that this bug was resolved.
>     However, yesterday, following an update, the problem reappeared.
>     Again,the workaround was to use the 5.0.2 version of
>     formats-gpl.
>
>     I have not had a chance to search my recent backups for this file
>     to see if I can determine exactly when it broke again -- I will
>     try to do that.
>
>
>     Best regards,
>     --aryeh
>
>
>
>             On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
>
>                 Hi Aryeh,
>
>                     How can I turn this into the formats-gpl.jar file?
>
>                 Great question! I'm cc'ing the list because I think
>                 this information is of
>                 general interest.
>
>                 The Bio-Formats site has a page with instructions for
>                 downloading and
>                 building the jars from source:
>                 https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html
>
>
>                 After cloning the Bio-Formats repository
>                 <http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
>
>                 you can either:
>                 * Check out a specific tag
>                 <http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
>
>                 or
>                 * Check out a specific commit
>                 <http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>
>
>                 Or it should be fine to just build the "develop"
>                 branch, since the patch in
>                 question was merged.
>
>                 After building Bio-Formats, all the output .jars will
>                 be in the /artifacts
>                 sub-directory of your Bio-Formats checkout.
>
>                 Let me know if you have any more questions, and thank
>                 you for taking the
>                 time to test this!
>
>                 Regards,
>                 Mark
>
>
>                 On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss
>                 <[hidden email] <mailto:[hidden email]>> wrote:
>
>                     Hi Mark
>
>                     On 10/1/14, 10:21 PM, Mark Hiner wrote:
>
>                         Hi Christophe,
>
>                           As far as I understand, the current dailies
>                         are 5.0, not 5.1 yet
>                         You are correct. We will be switching over to
>                         5.1.x, but in the mean time
>                         it looks like the nd2 fix
>                         <https://github.com/openmicroscopy/bioformats/commit/
>                         3c857c2e5743e9b23801408bd61de49697716b4d>
>                         you're looking for only affected the
>                         formats-gpl component. You should be
>                         able to just download that specific jar, and
>                         replace the
>                         formats-gpl-5.0.5.jar in your
>                         Fiji.app/jars/bioformats directory (the old
>                         version will just be called "formats-gpl.jar"
>                         if you still have the
>                         Bio-Formats update site enabled).
>
>                     How can I turn this into the formats-gpl.jar file?
>                     If I can do that, I will replace my version 5.0.2
>                     file, and see if it
>                     works properly
>
>                     thanks and best regards
>                     --aryeh
>
>
>
>
>
>
>     --
>     Aryeh Weiss
>     Faculty of Engineering
>     Bar Ilan University
>     Ramat Gan 52900 Israel
>
>     Ph:  972-3-5317638
>     FAX: [phone]
>
>     --
>     ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

This is a followup to OME bug 12548, ND@ reader issue.

I have been unable to comment in the OME bug tracking system, but as it
is relevant to Fiji, I am posting it here.

The latest update of Bio-formats still does not read my multifield ND2
files correctly. The problem still appears to be in formats-gpl.jar.
Replacing that with the 5.0.2 version still works.

I checking both the bioformats distributed by the bioformats update
site, and the bioformats distributed by the fiji update site.

I also downloaded the appropriate jar files from
ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
and tried those. The same problem occurs, except that
formats-gpl-5.0.2.jar does not work with the version 5.1 files.
Falling back to 5.0.6 _ the 5.0.2 formats-gpl still works.

On the OME tracking system, this bug is said to be resolved. If so, then
the corrected bioformats is not yet distributed on the fiji update sites.

--aryeh

On 12/6/14 7:27 PM, Aryeh Weiss wrote:

> On 12/6/14, 12:16 AM, Curtis Rueden wrote:
>> Hi Aryeh,
>>
>> > About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
>> > updater to update formats-gpl. The updated version correctly read my
>> > multifield ND2, so I thought that this bug was resolved. However,
>> > yesterday, following an update, the problem reappeared. Again,the
>> > workaround was to use the 5.0.2 version of formats-gpl.
>>
>> That is very odd. It would be great if you could somehow isolate the
>> difference between the working version of Fiji vs. the non-working
>> one—especially if they both used Bio-Formats 5.0.6.
>>
> I checked my backups, and I have been unable to find a working updated
> bioformats-gpl in my recent backups. This most likely means that I was
> mistaken about the problem being temporarily fixed.
>> What happens if you enable the Bio-Formats update site? Still non-working?
>>
> It fails both ways.
> Here is the info form teh advanced mode of the updater for the two
> bioformats-gpl files:
>
> bioformats from fiji site
> bioformats-gpl-5.0.6
> Modified 11 Nov 2014
>
> bioformats from bioformats site
> bioformats-gpl
> Modified 04 Nov 2014
>
> Both fail the same way.
>> If you get a chance, you could also test with the "showinf" command
>> line tool [1], which would rule out any Fiji-specific installation
>> issues. And of course testing from multiple different machines might
>> also shed some light on things.
>>
> The showinf output has the same error -- it is not Fiji specific.
> I can also tell you that the same problem occurs on a Windows 7-64bit
> OS, and the workaroudn is identical (fall back to gpl-5.0.2
>
> As long as the workaround works, it is ok. However, that seems like
> living on borrowed time...
>> Regards,
>> Curtis
>>
> Thank you for your attention to this.
>
> Best regards,
> --aryeh
>
>> [1]
>> http://openmicroscopy.org/site/support/bio-formats5/users/comlinetools/
>>
>> On Thu, Nov 27, 2014 at 1:45 AM, Aryeh Weiss <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>     On 10/6/14, 11:17 PM, Aryeh Weiss wrote:
>>
>>         Hi Melissa
>>
>>         On 10/6/14, 4:27 PM, Melissa Linkert wrote:
>>
>>             Hi Aryeh,
>>
>>                         You are correct. We will be switching over to
>>                         5.1.x, but in the mean time
>>                         it looks like the nd2 fix
>>                         <https://github.com/openmicroscopy/bioformats/commit/
>>                         3c857c2e5743e9b23801408bd61de49697716b4d>
>>                         you're looking for only affected the
>>                         formats-gpl component. You should be
>>                         able to just download that specific jar, and
>>                         replace the
>>                         formats-gpl-5.0.5.jar in your
>>                         Fiji.app/jars/bioformats directory (the old
>>                         version will just be called "formats-gpl.jar"
>>                         if you still have the
>>                         Bio-Formats update site enabled).
>>
>>                     How can I turn this into the formats-gpl.jar file?
>>                     If I can do that, I will replace my version 5.0.2
>>                     file, and see if it
>>                     works properly
>>
>>             Instead of compiling from source, you can also download
>>             the latest 5.1
>>             builds from:
>>
>>             http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
>>
>>
>>             For anyone trying this though, please do note that mixing
>>             5.1 and 5.0
>>             files is not supported and very unlikely to work, so you
>>             will need to
>>             update all files to 5.1.  Be aware that this can cause
>>             problems with
>>             other plugins that use Bio-Formats, as there are API
>>             differences between
>>             the two versions (though we have not yet released 5.1.0).
>>
>>
>>         Thank you (and also Mark) for your replies.
>>         I downloaded the  5.1 builds for all of the jar files in the
>>         jars/bio-formats directory of my Fiji distribution.
>>         When I dragged one of my nd2 files into Fiji, bio-formats
>>         opened, but had the same bug as reported previously.
>>         When I restored the old bio-formats directory with the 5.0.2
>>         version of gpl, it worked properly.
>>         I did not try the 5.0.2 gpl with the 5.1 release, because of
>>         Melissa warning concerning mixing the two versions.
>>
>>
>>         Best regards
>>         --aryeh
>>
>>
>>             We are also considering this fix for a 5.0.6 release of
>>             Bio-Formats, which
>>             would eliminate the need to manually update files.
>>
>>             Regards,
>>             -Melissa
>>
>>
>>     About two weeks ago, when 5.0.6 was announced, I allowed the Fiji
>>     updater to update formats-gpl.
>>     The updated version correctly read my multifield ND2, so I thought
>>     that this bug was resolved.
>>     However, yesterday, following an update, the problem reappeared.
>>     Again,the workaround was to use the 5.0.2 version of
>>     formats-gpl.
>>
>>     I have not had a chance to search my recent backups for this file
>>     to see if I can determine exactly when it broke again -- I will
>>     try to do that.
>>
>>
>>     Best regards,
>>     --aryeh
>>
>>
>>
>>             On Mon, Oct 06, 2014 at 07:52:39AM -0500, Mark Hiner wrote:
>>
>>                 Hi Aryeh,
>>
>>                     How can I turn this into the formats-gpl.jar file?
>>
>>                 Great question! I'm cc'ing the list because I think
>>                 this information is of
>>                 general interest.
>>
>>                 The Bio-Formats site has a page with instructions for
>>                 downloading and
>>                 building the jars from source:
>>                 https://www.openmicroscopy.org/site/support/bio-formats5/developers/building-bioformats.html
>>
>>
>>                 After cloning the Bio-Formats repository
>>                 <http://git-scm.com/book/en/Git-Basics-Getting-a-Git-Repository#Cloning-an-Existing-Repository>,
>>
>>                 you can either:
>>                 * Check out a specific tag
>>                 <http://stackoverflow.com/questions/791959/download-a-specific-tag-with-git>
>>
>>                 or
>>                 * Check out a specific commit
>>                 <http://stackoverflow.com/questions/2007662/rollback-to-an-old-commit-using-git>
>>
>>
>>                 Or it should be fine to just build the "develop"
>>                 branch, since the patch in
>>                 question was merged.
>>
>>                 After building Bio-Formats, all the output .jars will
>>                 be in the /artifacts
>>                 sub-directory of your Bio-Formats checkout.
>>
>>                 Let me know if you have any more questions, and thank
>>                 you for taking the
>>                 time to test this!
>>
>>                 Regards,
>>                 Mark
>>
>>
>>                 On Sat, Oct 4, 2014 at 3:03 PM, Aryeh Weiss
>>                 <[hidden email] <mailto:[hidden email]>> wrote:
>>
>>                     Hi Mark
>>
>>                     On 10/1/14, 10:21 PM, Mark Hiner wrote:
>>
>>                         Hi Christophe,
>>
>>                           As far as I understand, the current dailies
>>                         are 5.0, not 5.1 yet
>>                         You are correct. We will be switching over to
>>                         5.1.x, but in the mean time
>>                         it looks like the nd2 fix
>>                         <https://github.com/openmicroscopy/bioformats/commit/
>>                         3c857c2e5743e9b23801408bd61de49697716b4d>
>>                         you're looking for only affected the
>>                         formats-gpl component. You should be
>>                         able to just download that specific jar, and
>>                         replace the
>>                         formats-gpl-5.0.5.jar in your
>>                         Fiji.app/jars/bioformats directory (the old
>>                         version will just be called "formats-gpl.jar"
>>                         if you still have the
>>                         Bio-Formats update site enabled).
>>
>>                     How can I turn this into the formats-gpl.jar file?
>>                     If I can do that, I will replace my version 5.0.2
>>                     file, and see if it
>>                     works properly
>>
>>                     thanks and best regards
>>                     --aryeh
>>
>>
>>
>>
>>
>>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Mark Hiner]

Hi Aryeh,

Thanks for following up on the ImageJ list.

For reference:
- the closed ticket[1]
- commit on develop[2] (Bio-Formats 5.1.x)

>On the OME tracking system, this bug is said to be resolved. If so, then
the corrected bioformats is not yet distributed on the fiji update sites.

Fiji uses Bio-Formats 5.0.x, with the dev version[3] available from the
Bio-Formats development update site[4]. This fix will become part of core
Fiji when there's a 5.1.0 release.

>I also downloaded the appropriate jar files from
>ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
<http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>

I believe this was the correct place to pull artifacts from to test the ND2
fix, but you should not use 5.0.x jars with 5.1.x. If you want to try
5.1.x, you should replace everything in Fiji.app/jars/bio-formats with its
5.1.x equivalent.

Hope that helps. Good luck!

Best,
Mark

[1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
[2]
https://github.com/openmicroscopy/bioformats/commit/6e6387f8206889b416fe4df9f61d72f782ca0e9e
[3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
[4] http://imagej.net/List_of_update_sites

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Knecht, David]

Hi Mark- Has there been any progress on opening ND2 files with multiple positions?  I suggested a “split positions” checkbox a while back, but that seems to not have been implemented.    If there is no Z, the system interprets positions as z slices.   At this point, I don’t know a way to open multichannel, multi-z, multi position datasets other than to split them in Elements. Dave

On Feb 2, 2015, at 9:51 AM, Mark Hiner <[hidden email]> wrote:

> Hi Aryeh,
>
> Thanks for following up on the ImageJ list.
>
> For reference:
> - the closed ticket[1]
> - commit on develop[2] (Bio-Formats 5.1.x)
>
>> On the OME tracking system, this bug is said to be resolved. If so, then
> the corrected bioformats is not yet distributed on the fiji update sites.
>
> Fiji uses Bio-Formats 5.0.x, with the dev version[3] available from the
> Bio-Formats development update site[4]. This fix will become part of core
> Fiji when there's a 5.1.0 release.
>
>> I also downloaded the appropriate jar files from
>> ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
> <http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>
>
> I believe this was the correct place to pull artifacts from to test the ND2
> fix, but you should not use 5.0.x jars with 5.1.x. If you want to try
> 5.1.x, you should replace everything in Fiji.app/jars/bio-formats with its
> 5.1.x equivalent.
>
> Hope that helps. Good luck!
>
> Best,
> Mark
>
> [1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
> [2]
> https://github.com/openmicroscopy/bioformats/commit/6e6387f8206889b416fe4df9f61d72f782ca0e9e
> [3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
> [4] http://imagej.net/List_of_update_sites
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

Dr. David Knecht
Professor of Molecular and Cell Biology
Core Microscopy Facility Director
University of Connecticut
Storrs, CT 06269
860-486-2200

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Hi Mark

Thank you for your quick reply.

On 2/2/15 4:51 PM, Mark Hiner wrote:

> Hi Aryeh,
>
> Thanks for following up on the ImageJ list.
>
> For reference:
> - the closed ticket[1]
> - commit on develop[2] (Bio-Formats 5.1.x)
>
> >On the OME tracking system, this bug is said to be resolved. If so,
> then the corrected bioformats is not yet distributed on the fiji
> update sites.
>
> Fiji uses Bio-Formats 5.0.x, with the dev version[3] available from
> the Bio-Formats development update site[4]. This fix will become part
> of core Fiji when there's a 5.1.0 release.
>
> >I also downloaded the appropriate jar files from
> >ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
> <http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>
>
> I believe this was the correct place to pull artifacts from to test
> the ND2 fix, but you should not use 5.0.x jars with 5.1.x. If you want
> to try 5.1.x, you should replace everything in
> Fiji.app/jars/bio-formats with its 5.1.x equivalent.
>

I replaced all of the files. The 5.1 gpl file did not work at all with
the 5.0.6 files -- it threw an exception. So I downloaded the entire
5.1.x set and replaced all of the files in jars/bioformats. This worked
in the sense that it did not throw an exception, but it produced the
same incorrect loading of the multifield ND2 file.

Best regards,
--aryeh

> Hope that helps. Good luck!
>
> Best,
> Mark
>
> [1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
> [2]
> https://github.com/openmicroscopy/bioformats/commit/6e6387f8206889b416fe4df9f61d72f782ca0e9e
> [3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
> [4] http://imagej.net/List_of_update_sites

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

On 2/2/15 5:00 PM, Knecht, David wrote:
> Hi Mark- Has there been any progress on opening ND2 files with multiple positions?  I suggested a “split positions” checkbox a while back, but that seems to not have been implemented.    If there is no Z, the system interprets positions as z slices.   At this point, I don’t know a way to open multichannel, multi-z, multi position datasets other than to split them in Elements. Dave
>
> On Feb 2, 2015, at 9:51 AM, Mark Hiner <[hidden email]> wrote:

Hi David

You can open multifield ND2 files with bioformats. What you need to maek
it work correctly is the formats-gpl05.0.2.jar file, which still works
correctly with the 5.0.6 distribution. After you insert that, you should
make sure that it does not get updated when you update Fiji.

I can send it to you offlist if you want it. Insert it into
jars/bioformats , and make sure to remove the existing file.

With this workaround, I opened a file with 20 fields, each of which has
3 channels an 17 z-positions.

Best regards,
--aryeh

>> Hi Aryeh,
>>
>> Thanks for following up on the ImageJ list.
>>
>> For reference:
>> - the closed ticket[1]
>> - commit on develop[2] (Bio-Formats 5.1.x)
>>
>>> On the OME tracking system, this bug is said to be resolved. If so, then
>> the corrected bioformats is not yet distributed on the fiji update sites.
>>
>> Fiji uses Bio-Formats 5.0.x, with the dev version[3] available from the
>> Bio-Formats development update site[4]. This fix will become part of core
>> Fiji when there's a 5.1.0 release.
>>
>>> I also downloaded the appropriate jar files from
>>> ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
>> <http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>
>>
>> I believe this was the correct place to pull artifacts from to test the ND2
>> fix, but you should not use 5.0.x jars with 5.1.x. If you want to try
>> 5.1.x, you should replace everything in Fiji.app/jars/bio-formats with its
>> 5.1.x equivalent.
>>
>> Hope that helps. Good luck!
>>
>> Best,
>> Mark
>>
>> [1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
>> [2]
>> https://github.com/openmicroscopy/bioformats/commit/6e6387f8206889b416fe4df9f61d72f782ca0e9e
>> [3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
>> [4] http://imagej.net/List_of_update_sites
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> Dr. David Knecht
> Professor of Molecular and Cell Biology
> Core Microscopy Facility Director
> University of Connecticut
> Storrs, CT 06269
> 860-486-2200
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Aryeh,

> The latest update of Bio-formats still does not read my multifield ND2
> files correctly.

Very sorry to hear that there are still problems reading your data.

I spoke with Melissa briefly about this issue. The OME developers will need
a sample non-working dataset in order to debug the issue. The best place to
follow up is via the OME support channels:

- http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
- http://qa.openmicroscopy.org.uk/qa/upload/

Regards,
Curtis

On Mon, Feb 2, 2015 at 10:48 AM, Aryeh Weiss <[hidden email]> wrote:

> On 2/2/15 5:00 PM, Knecht, David wrote:
>
>> Hi Mark- Has there been any progress on opening ND2 files with multiple
>> positions?  I suggested a “split positions” checkbox a while back, but that
>> seems to not have been implemented.    If there is no Z, the system
>> interprets positions as z slices.   At this point, I don’t know a way to
>> open multichannel, multi-z, multi position datasets other than to split
>> them in Elements. Dave
>>
>> On Feb 2, 2015, at 9:51 AM, Mark Hiner <[hidden email]> wrote:
>>
>
> Hi David
>
> You can open multifield ND2 files with bioformats. What you need to maek
> it work correctly is the formats-gpl05.0.2.jar file, which still works
> correctly with the 5.0.6 distribution. After you insert that, you should
> make sure that it does not get updated when you update Fiji.
>
> I can send it to you offlist if you want it. Insert it into
> jars/bioformats , and make sure to remove the existing file.
>
> With this workaround, I opened a file with 20 fields, each of which has 3
> channels an 17 z-positions.
>
> Best regards,
> --aryeh
>
>
>
>  Hi Aryeh,
>>>
>>> Thanks for following up on the ImageJ list.
>>>
>>> For reference:
>>> - the closed ticket[1]
>>> - commit on develop[2] (Bio-Formats 5.1.x)
>>>
>>>  On the OME tracking system, this bug is said to be resolved. If so, then
>>>>
>>> the corrected bioformats is not yet distributed on the fiji update sites.
>>>
>>> Fiji uses Bio-Formats 5.0.x, with the dev version[3] available from the
>>> Bio-Formats development update site[4]. This fix will become part of core
>>> Fiji when there's a 5.1.0 release.
>>>
>>>  I also downloaded the appropriate jar files from
>>>> ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.
>>>> 1-latest/lastSuccessfulBuild/artifact/artifacts/
>>>>
>>> <http://ci.openmicroscopy.org/view/Bio-Formats/job/
>>> BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>
>>>
>>> I believe this was the correct place to pull artifacts from to test the
>>> ND2
>>> fix, but you should not use 5.0.x jars with 5.1.x. If you want to try
>>> 5.1.x, you should replace everything in Fiji.app/jars/bio-formats with
>>> its
>>> 5.1.x equivalent.
>>>
>>> Hope that helps. Good luck!
>>>
>>> Best,
>>> Mark
>>>
>>> [1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
>>> [2]
>>> https://github.com/openmicroscopy/bioformats/commit/
>>> 6e6387f8206889b416fe4df9f61d72f782ca0e9e
>>> [3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
>>> [4] http://imagej.net/List_of_update_sites
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>> Dr. David Knecht
>> Professor of Molecular and Cell Biology
>> Core Microscopy Facility Director
>> University of Connecticut
>> Storrs, CT 06269
>> 860-486-2200
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Aryeh Weiss]

Hi Curtiss

I uploaded an rather large file when I first reported this. Since the
files are quite large  (2-4GB), please let me know if you still have
that one before I upload another one. I cannot do an upload of that size
from home.

Best regards
--aryeh

On 2/2/15 7:35 PM, Curtis Rueden wrote:

> Hi Aryeh,
>
> > The latest update of Bio-formats still does not read my multifield ND2
> > files correctly.
>
> Very sorry to hear that there are still problems reading your data.
>
> I spoke with Melissa briefly about this issue. The OME developers will
> need a sample non-working dataset in order to debug the issue. The
> best place to follow up is via the OME support channels:
>
> - http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users/
> - http://qa.openmicroscopy.org.uk/qa/upload/
>
> Regards,
> Curtis
>
> On Mon, Feb 2, 2015 at 10:48 AM, Aryeh Weiss <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     On 2/2/15 5:00 PM, Knecht, David wrote:
>
>         Hi Mark- Has there been any progress on opening ND2 files with
>         multiple positions?  I suggested a “split positions” checkbox
>         a while back, but that seems to not have been implemented.  
>         If there is no Z, the system interprets positions as z
>         slices.   At this point, I don’t know a way to open
>         multichannel, multi-z, multi position datasets other than to
>         split them in Elements. Dave
>
>         On Feb 2, 2015, at 9:51 AM, Mark Hiner <[hidden email]
>         <mailto:[hidden email]>> wrote:
>
>
>     Hi David
>
>     You can open multifield ND2 files with bioformats. What you need
>     to maek it work correctly is the formats-gpl05.0.2.jar file, which
>     still works correctly with the 5.0.6 distribution. After you
>     insert that, you should make sure that it does not get updated
>     when you update Fiji.
>
>     I can send it to you offlist if you want it. Insert it into
>     jars/bioformats , and make sure to remove the existing file.
>
>     With this workaround, I opened a file with 20 fields, each of
>     which has 3 channels an 17 z-positions.
>
>     Best regards,
>     --aryeh
>
>
>
>             Hi Aryeh,
>
>             Thanks for following up on the ImageJ list.
>
>             For reference:
>             - the closed ticket[1]
>             - commit on develop[2] (Bio-Formats 5.1.x)
>
>                 On the OME tracking system, this bug is said to be
>                 resolved. If so, then
>
>             the corrected bioformats is not yet distributed on the
>             fiji update sites.
>
>             Fiji uses Bio-Formats 5.0.x, with the dev version[3]
>             available from the
>             Bio-Formats development update site[4]. This fix will
>             become part of core
>             Fiji when there's a 5.1.0 release.
>
>                 I also downloaded the appropriate jar files from
>                 ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/
>                 <http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>
>
>             <http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/>
>
>             I believe this was the correct place to pull artifacts
>             from to test the ND2
>             fix, but you should not use 5.0.x jars with 5.1.x. If you
>             want to try
>             5.1.x, you should replace everything in
>             Fiji.app/jars/bio-formats with its
>             5.1.x equivalent.
>
>             Hope that helps. Good luck!
>
>             Best,
>             Mark
>
>             [1] http://trac.openmicroscopy.org.uk/ome/ticket/12548
>             [2]
>             https://github.com/openmicroscopy/bioformats/commit/6e6387f8206889b416fe4df9f61d72f782ca0e9e
>             [3] https://github.com/openmicroscopy/bioformats/tree/dev_5_0
>             [4] http://imagej.net/List_of_update_sites
>
>             --
>             ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>         Dr. David Knecht
>         Professor of Molecular and Cell Biology
>         Core Microscopy Facility Director
>         University of Connecticut
>         Storrs, CT 06269
>         860-486-2200 <tel:[phone]>
>
>         --
>         ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
>
>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]


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