Very slow opening of stacks in Fiji

[GeraldT]

Dear List members:

I am using Fiji with the latest updates (ImageJ2 components). I work a lot with stacks (DICOM files, mostly 1k*1k resolution, 16 bit, 150 - 800 slices/images).
I open them dragging the folder containing the files and dropping them on the Fiji window. It takes now very long time (minutes) to open such a slice vs seconds in ImageJ (original). It has been like that for a while. I think it has something to do with the ImageJ2 components?

Mvh
Gerald R. Torgersen
IT-seksjonen,
Det odontologiske fakultet / Faculty of Dentistry
Universitetet i Oslo / University of Oslo

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[Mark Hiner]

Hi Gerald,

 Yes, there are several known performance issues in the ImageJ2 components,
many of which are still in beta and unoptimized. For typical users, all
options under "Edit > Options > ImageJ2" should be disabled while we work
to move these products towards a release state. These options should have
been disabled by default; please let us know if they were not.

Regards,
Mark

On Mon, Oct 13, 2014 at 7:32 AM, Gerald Ruiner Torgersen <
[hidden email]> wrote:

> Dear List members:
>
> I am using Fiji with the latest updates (ImageJ2 components). I work a lot
> with stacks (DICOM files, mostly 1k*1k resolution, 16 bit, 150 - 800
> slices/images).
> I open them dragging the folder containing the files and dropping them on
> the Fiji window. It takes now very long time (minutes) to open such a slice
> vs seconds in ImageJ (original). It has been like that for a while. I think
> it has something to do with the ImageJ2 components?
>
> Mvh
> Gerald R. Torgersen
> IT-seksjonen,
> Det odontologiske fakultet / Faculty of Dentistry
> Universitetet i Oslo / University of Oslo
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[GeraldT]

Thank you Mark,

I have enabled them manually because of the better support of DICOM i IJ2. But the files I am working with recently are not compressed, så IJ1 opens them.
With SCIFIO disabled Fiji is as quick as ImageJ. The problem is that DICOM stacks get sorted the wrong way in original ImageJ. This works right in SCIFIO.
Looking forward to see the release with all issues fixed :-)

Greetings
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Mark Hiner
>Sent: Monday, October 13, 2014 3:20 PM
>To: [hidden email]
>Subject: Re: Very slow opening of stacks in Fiji
>
>Hi Gerald,
>
> Yes, there are several known performance issues in the ImageJ2 components,
>many of which are still in beta and unoptimized. For typical users, all options
>under "Edit > Options > ImageJ2" should be disabled while we work to move
>these products towards a release state. These options should have been
>disabled by default; please let us know if they were not.
>
>Regards,
>Mark
>
>On Mon, Oct 13, 2014 at 7:32 AM, Gerald Ruiner Torgersen <
>[hidden email]> wrote:
>
>> Dear List members:
>>
>> I am using Fiji with the latest updates (ImageJ2 components). I work a
>> lot with stacks (DICOM files, mostly 1k*1k resolution, 16 bit, 150 -
>> 800 slices/images).
>> I open them dragging the folder containing the files and dropping them
>> on the Fiji window. It takes now very long time (minutes) to open such
>> a slice vs seconds in ImageJ (original). It has been like that for a
>> while. I think it has something to do with the ImageJ2 components?
>>
>> Mvh
>> Gerald R. Torgersen
>> IT-seksjonen,
>> Det odontologiske fakultet / Faculty of Dentistry Universitetet i Oslo
>> / University of Oslo
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
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>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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[Mark Hiner]

Hi Gerald,

 Very happy to hear your data is at least opening correctly in SCIFIO! Just
wanted to say thank you for providing feedback. :) Hope we can get some of
the performance issues resolved soon.

Thanks again,
Mark

On Mon, Oct 13, 2014 at 8:26 AM, Gerald Ruiner Torgersen <
[hidden email]> wrote:

> Thank you Mark,
>
> I have enabled them manually because of the better support of DICOM i IJ2.
> But the files I am working with recently are not compressed, så IJ1 opens
> them.
> With SCIFIO disabled Fiji is as quick as ImageJ. The problem is that DICOM
> stacks get sorted the wrong way in original ImageJ. This works right in
> SCIFIO.
> Looking forward to see the release with all issues fixed :-)
>
> Greetings
> Gerald R. Torgersen
>
>
> >-----Original Message-----
> >From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> >Mark Hiner
> >Sent: Monday, October 13, 2014 3:20 PM
> >To: [hidden email]
> >Subject: Re: Very slow opening of stacks in Fiji
> >
> >Hi Gerald,
> >
> > Yes, there are several known performance issues in the ImageJ2
> components,
> >many of which are still in beta and unoptimized. For typical users, all
> options
> >under "Edit > Options > ImageJ2" should be disabled while we work to move
> >these products towards a release state. These options should have been
> >disabled by default; please let us know if they were not.
> >
> >Regards,
> >Mark
> >
> >On Mon, Oct 13, 2014 at 7:32 AM, Gerald Ruiner Torgersen <
> >[hidden email]> wrote:
> >
> >> Dear List members:
> >>
> >> I am using Fiji with the latest updates (ImageJ2 components). I work a
> >> lot with stacks (DICOM files, mostly 1k*1k resolution, 16 bit, 150 -
> >> 800 slices/images).
> >> I open them dragging the folder containing the files and dropping them
> >> on the Fiji window. It takes now very long time (minutes) to open such
> >> a slice vs seconds in ImageJ (original). It has been like that for a
> >> while. I think it has something to do with the ImageJ2 components?
> >>
> >> Mvh
> >> Gerald R. Torgersen
> >> IT-seksjonen,
> >> Det odontologiske fakultet / Faculty of Dentistry Universitetet i Oslo
> >> / University of Oslo
> >>
> >> --
> >> 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
>

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[GeraldT]

Hi again,

a little correction: It looks like only the stacks from one manufacturer have problems with slice order. It is the brand I use most in my research, so I had the impression that the problem is more common. Still they open correctly with Scifio.

Mvh
Gerald R. Torgersen

>-----Original Message-----
>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>Gerald Ruiner Torgersen
>Sent: Monday, October 13, 2014 3:27 PM
>To: [hidden email]
>Subject: Re: Very slow opening of stacks in Fiji
>
>Thank you Mark,
>
>I have enabled them manually because of the better support of DICOM i IJ2.
>But the files I am working with recently are not compressed, så IJ1 opens
>them.
>With SCIFIO disabled Fiji is as quick as ImageJ. The problem is that DICOM
>stacks get sorted the wrong way in original ImageJ. This works right in SCIFIO.
>Looking forward to see the release with all issues fixed :-)
>
>Greetings
>Gerald R. Torgersen
>
>
>>-----Original Message-----
>>From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
>>Mark Hiner
>>Sent: Monday, October 13, 2014 3:20 PM
>>To: [hidden email]
>>Subject: Re: Very slow opening of stacks in Fiji
>>
>>Hi Gerald,
>>
>> Yes, there are several known performance issues in the ImageJ2
>>components, many of which are still in beta and unoptimized. For
>>typical users, all options under "Edit > Options > ImageJ2" should be
>>disabled while we work to move these products towards a release state.
>>These options should have been disabled by default; please let us know if
>they were not.
>>
>>Regards,
>>Mark
>>
>>On Mon, Oct 13, 2014 at 7:32 AM, Gerald Ruiner Torgersen <
>>[hidden email]> wrote:
>>
>>> Dear List members:
>>>
>>> I am using Fiji with the latest updates (ImageJ2 components). I work
>>> a lot with stacks (DICOM files, mostly 1k*1k resolution, 16 bit, 150
>>> -
>>> 800 slices/images).
>>> I open them dragging the folder containing the files and dropping
>>> them on the Fiji window. It takes now very long time (minutes) to
>>> open such a slice vs seconds in ImageJ (original). It has been like
>>> that for a while. I think it has something to do with the ImageJ2
>components?
>>>
>>> Mvh
>>> Gerald R. Torgersen
>>> IT-seksjonen,
>>> Det odontologiske fakultet / Faculty of Dentistry Universitetet i
>>> Oslo / University of Oslo
>>>
>>> --
>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>>
>>
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>>ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
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>ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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