"Analyse particles" does never start for stack analysis

[Joce]

Dear everyone

I'm using the "Analyse particle" function from the "Analyse" menu on images
which I have thresholded.
When doing it on a single image, this works fine ; however with a whole
stack, ImageJ seems to give up after asking wether it should process the
whole stack : the dialog "Process all N images?" appears, I click Yes,
and... nothing ever happens.

This doesn't work either with the stack from sample "Bat Cochlea Volume".

However, if I duplicate just the first image from a stack, and run Analyse
particles on it, I get the result and drawing of outline if I asked for it,
for that single image. But trying to do the same duplicating a few images,
it still stops after the dialog "Process all N images?", and I don't even
get the "save measurements" dialog.

The funny thing is that I used to do that in just the same way and got the
analysis to work, on the same data. I've tried versions 1.43l, 1.43o and
1.43r on 2 different computers with different linux install on which this
used to work. I've tried moving away my ~/.imagej configuration directory.
To no avail...

Any idea of what may be going wrong or what I may be doing wrong?
Cheers.
Jocelyn

--
Jocelyn Etienne  ---  Research Fellow of the CNRS  ---  [phone]
Laboratoire de Spectrometrie Physique,  Université J. Fourier Grenoble I
[hidden email]     http://www-lsp.ujf-grenoble.fr/link/etienne

[Aryeh Weiss]

This sounds similar to something that happened to me with Fiji, but it
turned out to be a problem with the Java installation. Try downloading
and running JavaSUN instead of OpenJava. (I was using Suse 11.2, and
they note that for copyright reasons, they did not distribute JavaSun,
but you can download and install it with Yast).

--aryeh

On 8/30/10 5:01 PM, Jocelyn ETIENNE wrote:

> Dear everyone
>
> I'm using the "Analyse particle" function from the "Analyse" menu on images
> which I have thresholded.
> When doing it on a single image, this works fine ; however with a whole
> stack, ImageJ seems to give up after asking wether it should process the
> whole stack : the dialog "Process all N images?" appears, I click Yes,
> and... nothing ever happens.
>
> This doesn't work either with the stack from sample "Bat Cochlea Volume".
>
> However, if I duplicate just the first image from a stack, and run Analyse
> particles on it, I get the result and drawing of outline if I asked for it,
> for that single image. But trying to do the same duplicating a few images,
> it still stops after the dialog "Process all N images?", and I don't even
> get the "save measurements" dialog.
>
> The funny thing is that I used to do that in just the same way and got the
> analysis to work, on the same data. I've tried versions 1.43l, 1.43o and
> 1.43r on 2 different computers with different linux install on which this
> used to work. I've tried moving away my ~/.imagej configuration directory.
> To no avail...
>
> Any idea of what may be going wrong or what I may be doing wrong?
> Cheers.
> Jocelyn
>

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

Ph:  972-3-5317638
FAX: [phone]

[Joce]

Thanks to all and to Aryeh especially -- it turns out that it was an
OpenJava problem. Funny since it used to work and I don't remember
having changer version for either OpenJava or ImageJ.

Best regards
Jocelyn

On Mon 30 Aug at 22:07 +0300, Aryeh Weiss <[hidden email]> wrote :

> This sounds similar to something that happened to me with Fiji, but it  
> turned out to be a problem with the Java installation. Try downloading  
> and running JavaSUN instead of OpenJava. (I was using Suse 11.2, and  
> they note that for copyright reasons, they did not distribute JavaSun,
> but you can download and install it with Yast).
>
> --aryeh
>
> On 8/30/10 5:01 PM, Jocelyn ETIENNE wrote:
>> Dear everyone
>>
>> I'm using the "Analyse particle" function from the "Analyse" menu on images
>> which I have thresholded.
>> When doing it on a single image, this works fine ; however with a whole
>> stack, ImageJ seems to give up after asking wether it should process the
>> whole stack : the dialog "Process all N images?" appears, I click Yes,
>> and... nothing ever happens.
>>
>> This doesn't work either with the stack from sample "Bat Cochlea Volume".
>>
>> However, if I duplicate just the first image from a stack, and run Analyse
>> particles on it, I get the result and drawing of outline if I asked for it,
>> for that single image. But trying to do the same duplicating a few images,
>> it still stops after the dialog "Process all N images?", and I don't even
>> get the "save measurements" dialog.
>>
>> The funny thing is that I used to do that in just the same way and got the
>> analysis to work, on the same data. I've tried versions 1.43l, 1.43o and
>> 1.43r on 2 different computers with different linux install on which this
>> used to work. I've tried moving away my ~/.imagej configuration directory.
>> To no avail...
>>
>> Any idea of what may be going wrong or what I may be doing wrong?
>> Cheers.
>> Jocelyn
>>
>
>
> --
> Aryeh Weiss
> School of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]

--
Jocelyn Etienne  ---  Research Fellow of the CNRS  ---  [phone]
Laboratoire de Spectrometrie Physique,  Université J. Fourier Grenoble I
[hidden email]     http://www-lsp.ujf-grenoble.fr/link/etienne

[Joce]

Dear all,

I'm setting a threshold for a whole stack of time-evolution images --
I'll be comparing the values obtained from these images, so I want the
same threshold for all: in the process, I set the threshold, then moves
to the window with my stack and check this threshold is satisfactory all
along the sequence.

But as I move back to the "Threshold" window in order to click Apply,
clicking on its frame, quite ofen the threshold gets auto-reset without
me asking for it -- and thus I loose my settings.

I'd consider it a bug. Does it happen for you?

Regards,
Jocelyn

[ved sharma-2]

Hi Jocelyn,

I had a similar situation when I was working with some 16-bit image stacks. In my case, I wanted to keep the upper threshold value = global maximum pixel value, and adjust the lower threshold value until it was OK for all the slices in the stack.

What I did was to first find out the slice which contains the maximum pixel value, bring the upper threshold to max, adjust the threshold of that slice, then go to all the other slices in the stack and adjust lower threshold value. After I found the minimum threshold value which works for all the slices, I clicked apply and it applied those min and max settings for all the slices.

Ved

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

On Sep 6, 2010, at 9:01 AM, Jocelyn ETIENNE wrote:

> Dear all,
>
> I'm setting a threshold for a whole stack of time-evolution images --
> I'll be comparing the values obtained from these images, so I want the
> same threshold for all: in the process, I set the threshold, then moves
> to the window with my stack and check this threshold is satisfactory all
> along the sequence.
>
> But as I move back to the "Threshold" window in order to click Apply,
> clicking on its frame, quite ofen the threshold gets auto-reset without
> me asking for it -- and thus I loose my settings.
>
> I'd consider it a bug. Does it happen for you?

This bug was fixed in ImageJ 1.42m.

    * 1.42m, 22 April 2009
        * Fixed a bug that caused the Image>Adjust>Threshold tool to
         override existing threshold settings of 16 and 32 bit images.

-wayne