hyperstack becomes a stack?

[Aryeh Weiss]

The following line uses the bioformats importer to open a multichannel
z-stack. It open as a hyperstack of 16-bit images.

run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
view=Hyperstack stack_order=XYCZT");

However, when I use:

run("8-bit");

That hyperstack is converted to an interleaved stack. This does not
happen if I do these operations manually.

Is this a bug, or did I miss something about how these operations work?

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

Ph:  972-3-5317638
FAX: [phone]

[Aryeh Weiss]

On 2/6/12 1:38 PM, Aryeh Weiss wrote:

> The following line uses the bioformats importer to open a multichannel
> z-stack. It open as a hyperstack of 16-bit images.
>
> run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
> view=Hyperstack stack_order=XYCZT");
>
> However, when I use:
>
> run("8-bit");
>
> That hyperstack is converted to an interleaved stack. This does not
> happen if I do these operations manually.
>
> Is this a bug, or did I miss something about how these operations work?
>
> --aryeh

run("crop");
does the same thing.
Inside the macro I get an interleaved stack.

Outside the macro (eg I insert exit(); after reading in the file), teh
hyperstack remains as a hyperstack.

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

Ph:  972-3-5317638
FAX: [phone]

[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 6, 2012, at 6:38 AM, Aryeh Weiss wrote:

> The following line uses the bioformats importer to open a multichannel
> z-stack. It open as a hyperstack of 16-bit images.
>
> run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
> view=Hyperstack stack_order=XYCZT");
>
> However, when I use:
>
> run("8-bit");
>
> That hyperstack is converted to an interleaved stack. This does not
> happen if I do these operations manually.
>
> Is this a bug, or did I miss something about how these operations work?

I am working on a fix for this timing-related bug. In the meantime, you can work around it by adding

  wait(1000);

to your macro just before

  run("8-bit");

-wayne

[Melissa Linkert-2]

Hi Aryeh,

> >The following line uses the bioformats importer to open a multichannel
> >z-stack. It open as a hyperstack of 16-bit images.
> >
> >run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
> >view=Hyperstack stack_order=XYCZT");
> >
> >However, when I use:
> >
> >run("8-bit");
> >
> >That hyperstack is converted to an interleaved stack. This does not
> >happen if I do these operations manually.
> >
> >Is this a bug, or did I miss something about how these operations work?

I don't know what causes this, but I was able to see the same behavior
using the following macro and ImageJ 1.46f:

-- begin --
run("Mitosis (26MB, 5D stack)");
run("8-bit");
-- end --

...in other words, it seems to be a problem with hyperstack handling in general
and not something in the Bio-Formats importer.

Regards,
-Melissa

On Mon, Feb 06, 2012 at 02:00:10PM +0200, Aryeh Weiss wrote:

> On 2/6/12 1:38 PM, Aryeh Weiss wrote:
> >The following line uses the bioformats importer to open a multichannel
> >z-stack. It open as a hyperstack of 16-bit images.
> >
> >run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
> >view=Hyperstack stack_order=XYCZT");
> >
> >However, when I use:
> >
> >run("8-bit");
> >
> >That hyperstack is converted to an interleaved stack. This does not
> >happen if I do these operations manually.
> >
> >Is this a bug, or did I miss something about how these operations work?
> >
> >--aryeh
>
> run("crop");
> does the same thing.
> Inside the macro I get an interleaved stack.
>
> Outside the macro (eg I insert exit(); after reading in the file),
> teh hyperstack remains as a hyperstack.
>
> --aryeh
> --
> Aryeh Weiss
> School of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]

[Aryeh Weiss]

On 2/6/12 4:37 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Feb 6, 2012, at 6:38 AM, Aryeh Weiss wrote:
>
>> The following line uses the bioformats importer to open a multichannel
>> z-stack. It open as a hyperstack of 16-bit images.
>>
>> run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
>> view=Hyperstack stack_order=XYCZT");
>>
>> However, when I use:
>>
>> run("8-bit");
>>
>> That hyperstack is converted to an interleaved stack. This does not
>> happen if I do these operations manually.
>>
>> Is this a bug, or did I miss something about how these operations work?
>
> I am working on a fix for this timing-related bug. In the meantime, you can work around it by adding
>
>    wait(1000);
>
> to your macro just before
>
>    run("8-bit");
>
> -wayne
>

Thank you for the quick response and work-around.
I tried it, and this solves my immediate problem.

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

Ph:  972-3-5317638
FAX: [phone]

[Rasband, Wayne (NIH/NIMH) [E]]

On Feb 6, 2012, at 6:38 AM, Aryeh Weiss wrote:

> The following line uses the bioformats importer to open a multichannel
> z-stack. It open as a hyperstack of 16-bit images.
>
> run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
> view=Hyperstack stack_order=XYCZT");
>
> However, when I use:
>
> run("8-bit");
>
> That hyperstack is converted to an interleaved stack. This does not
> happen if I do these operations manually.
>
> Is this a bug, or did I miss something about how these operations work?

This bug is fixed in the ImageJ 1.46g2 daily build. It was a timing-related problem with hyperstack handling in general, not with the Bio-Formats Importer. This macro code

   open(path_to_hyperstack);
   run("8-bit");

will trigger the bug, or this

    run("Mitosis (26MB, 5D stack)");
    makeRectangle(22, 26, 127, 142);
    run("Crop");

-wayne

[Aryeh Weiss]

On 2/6/12 9:47 PM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Feb 6, 2012, at 6:38 AM, Aryeh Weiss wrote:
>
>> The following line uses the bioformats importer to open a multichannel
>> z-stack. It open as a hyperstack of 16-bit images.
>>
>> run("Bio-Formats Importer", "open=[&path] autoscale color_mode=Default
>> view=Hyperstack stack_order=XYCZT");
>>
>> However, when I use:
>>
>> run("8-bit");
>>
>> That hyperstack is converted to an interleaved stack. This does not
>> happen if I do these operations manually.
>>
>> Is this a bug, or did I miss something about how these operations work?
>
> This bug is fixed in the ImageJ 1.46g2 daily build. It was a timing-related problem with hyperstack handling in general, not with the Bio-Formats Importer. This macro code
>
>     open(path_to_hyperstack);
>     run("8-bit");
>
> will trigger the bug, or this
>
>      run("Mitosis (26MB, 5D stack)");
>      makeRectangle(22, 26, 127, 142);
>      run("Crop");
>
> -wayne
>

Thank you for such quick attention to this issue.
I just upgraded to 1.46g2, and removed the wait statements.
However, the bug re-appeared.
Since this may be system dependent, I note that I am running the Fiji
distribution on a 2.66 GHz MacBook Pro running OSX 10.6.8.

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

Ph:  972-3-5317638
FAX: [phone]