Latest Bio-Formats in Fiji

[ctrueden]

Hi Aryeh,

> 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.

Thank you for the clarification. I have reopened ticket #12548 with your
and Dave's comments from this thread [1]. I expect that the data you
already uploaded is sufficient to continue investigating the issue; we will
let you know if not.

Regards,
Curtis

[1] https://trac.openmicroscopy.org.uk/ome/ticket/12548#comment:10


On Mon, Feb 2, 2015 at 12:05 PM, Aryeh Weiss <[hidden email]> wrote:

>  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]> 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

[Melissa Linkert-2]

Hi Aryeh,

> > 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.
>
> Thank you for the clarification. I have reopened ticket #12548 with your
> and Dave's comments from this thread [1]. I expect that the data you
> already uploaded is sufficient to continue investigating the issue; we will
> let you know if not.

You may have seen this already, but for anyone else following along:

http://trac.openmicroscopy.org/ome/ticket/12548#comment:11

I can confirm that the file you uploaded previously does open with the
correct stage position, Z section, and channel counts using the files
from http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/.  With versions of those files that pre-date the fixes mentioned in the ticket,
I do see the same dimensionality problems that you originally reported.

Please do make sure that all of the steps listed in the ticket comment
have been performed when updating your Fiji installation - it is really
easy to forget a file or miss a step.

If that still doesn't work, please upload a Zip file containing your
Fiji installation directory - this should help us to pinpoint any
problems that may have occurred during the update.

Regards,
-Melissa


On Mon, Feb 02, 2015 at 03:03:37PM -0600, Curtis Rueden wrote:

> Hi Aryeh,
>
> > 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.
>
> Thank you for the clarification. I have reopened ticket #12548 with your
> and Dave's comments from this thread [1]. I expect that the data you
> already uploaded is sufficient to continue investigating the issue; we will
> let you know if not.
>
> Regards,
> Curtis
>
> [1] https://trac.openmicroscopy.org.uk/ome/ticket/12548#comment:10
>
>
> On Mon, Feb 2, 2015 at 12:05 PM, Aryeh Weiss <[hidden email]> wrote:
>
> >  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]> 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

[Aryeh Weiss]

HI Melissa

Thank you for these explicit Instructions.
After doing this my multifield ND2 file loads correctly.

Best regards
--aryeh


On 2/5/15 10:52 PM, Melissa Linkert wrote:

> Hi Aryeh,
>
>>> 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.
>> Thank you for the clarification. I have reopened ticket #12548 with your
>> and Dave's comments from this thread [1]. I expect that the data you
>> already uploaded is sufficient to continue investigating the issue; we will
>> let you know if not.
> You may have seen this already, but for anyone else following along:
>
> http://trac.openmicroscopy.org/ome/ticket/12548#comment:11
>
> I can confirm that the file you uploaded previously does open with the
> correct stage position, Z section, and channel counts using the files
> from http://ci.openmicroscopy.org/view/Bio-Formats/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/.  With versions of those files that pre-date the fixes mentioned in the ticket,
> I do see the same dimensionality problems that you originally reported.
>
> Please do make sure that all of the steps listed in the ticket comment
> have been performed when updating your Fiji installation - it is really
> easy to forget a file or miss a step.
>
> If that still doesn't work, please upload a Zip file containing your
> Fiji installation directory - this should help us to pinpoint any
> problems that may have occurred during the update.
>
> Regards,
> -Melissa
>
>
> On Mon, Feb 02, 2015 at 03:03:37PM -0600, Curtis Rueden wrote:
>> Hi Aryeh,
>>
>>> 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.
>> Thank you for the clarification. I have reopened ticket #12548 with your
>> and Dave's comments from this thread [1]. I expect that the data you
>> already uploaded is sufficient to continue investigating the issue; we will
>> let you know if not.
>>
>> Regards,
>> Curtis
>>
>> [1] https://trac.openmicroscopy.org.uk/ome/ticket/12548#comment:10
>>
>>
>> On Mon, Feb 2, 2015 at 12:05 PM, Aryeh Weiss <[hidden email]> wrote:
>>
>>>   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]> 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