Recent bug at opening 16-bits series

[Gaelle Recher]

Dear ImageJ users and developers,

Since a couple of days when I open 16-bits series (z-stacks) there is a strange thing occurring: the stack is only composed of the first slice repeated.
(I have these data for quite a while and already been able to open them properly)
Does anyone had this same bug?
Do you have any idea of how to overcome this problem?

Thanks a lot!
Cheers,

Gaelle Recher

Research Associate
Magdalena Zernicka-Goetz Group

Department of Physiology, Development and Neuroscience & Gurdon Insitute
Downing Street, Cambridge, CB2 3DY, UK
Lab: [phone], gr373[a]cam.ac.uk
Gaëlle Recher


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[ctrueden]

Hi Gaelle,

> Since a couple of days when I open 16-bits series (z-stacks) there is
> a strange thing occurring: the stack is only composed of the first
> slice repeated. (I have these data for quite a while and already been
> able to open them properly)

I cannot replicate this problem with an up-to-date version of ImageJ. I
opened the MRI Stack sample, converted to 16-bit, multiplied the data
values by 4, saved as a 16-bit TIFF, and reopened the file, and all is
well. I tested with and without the SCIFIO feature enabled (Edit > Options
> ImageJ2, "Use SCIFIO when opening files").

Could you use the Help > Report a Bug command to submit a bug with your
system configuration (this includes a snapshot of your ImageJ
installation), and also please upload a sample non-working dataset using
Help > Upload Sample Image? The image will be kept confidential, used for
debugging purposes only.

Regards,
Curtis


On Mon, Jun 30, 2014 at 10:46 AM, Gaelle Recher <
[hidden email]> wrote:

> Dear ImageJ users and developers,
>
> Since a couple of days when I open 16-bits series (z-stacks) there is a
> strange thing occurring: the stack is only composed of the first slice
> repeated.
> (I have these data for quite a while and already been able to open them
> properly)
> Does anyone had this same bug?
> Do you have any idea of how to overcome this problem?
>
> Thanks a lot!
> Cheers,
>
> Gaelle Recher
>
> Research Associate
> Magdalena Zernicka-Goetz Group
>
> Department of Physiology, Development and Neuroscience & Gurdon Insitute
> Downing Street, Cambridge, CB2 3DY, UK
> Lab: [phone], gr373[a]cam.ac.uk
> Gaëlle Recher
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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

[Gaelle Recher]

Dear Curtis,

Thank you for answering,
I already had a separate answer by Wayne, and he also advise me to try to repeat make a bug report.
I actually use Fiji with SCIFIO option unchecked.

best,


Gaëlle Recher


Research Associate
Magdalena Zernicka-Goetz Group

Department of Physiology, Development and Neuroscience & Gurdon Insitute
Downing Street, Cambridge, CB2 3DY, UK
Lab: [phone], gr373[a]cam.ac.uk


Le 30 juin 2014 à 18:46, Curtis Rueden <[hidden email]> a écrit :

> Hi Gaelle,
>
>> Since a couple of days when I open 16-bits series (z-stacks) there is
>> a strange thing occurring: the stack is only composed of the first
>> slice repeated. (I have these data for quite a while and already been
>> able to open them properly)
>
> I cannot replicate this problem with an up-to-date version of ImageJ. I
> opened the MRI Stack sample, converted to 16-bit, multiplied the data
> values by 4, saved as a 16-bit TIFF, and reopened the file, and all is
> well. I tested with and without the SCIFIO feature enabled (Edit > Options
>> ImageJ2, "Use SCIFIO when opening files").
>
> Could you use the Help > Report a Bug command to submit a bug with your
> system configuration (this includes a snapshot of your ImageJ
> installation), and also please upload a sample non-working dataset using
> Help > Upload Sample Image? The image will be kept confidential, used for
> debugging purposes only.
>
> Regards,
> Curtis
>
>
> On Mon, Jun 30, 2014 at 10:46 AM, Gaelle Recher <
> [hidden email]> wrote:
>
>> Dear ImageJ users and developers,
>>
>> Since a couple of days when I open 16-bits series (z-stacks) there is a
>> strange thing occurring: the stack is only composed of the first slice
>> repeated.
>> (I have these data for quite a while and already been able to open them
>> properly)
>> Does anyone had this same bug?
>> Do you have any idea of how to overcome this problem?
>>
>> Thanks a lot!
>> Cheers,
>>
>> Gaelle Recher
>>
>> Research Associate
>> Magdalena Zernicka-Goetz Group
>>
>> Department of Physiology, Development and Neuroscience & Gurdon Insitute
>> Downing Street, Cambridge, CB2 3DY, UK
>> Lab: [phone], gr373[a]cam.ac.uk
>> Gaëlle Recher
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

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