volume measurement and memory problems

[Paola Lepanto]

Hi everyone,
I´ve been stuck with some problems: regarding the computer memory
problems, JRockit JMV is no longer available to extend the memory that
ImageJ can use in 32bits Windows, anybody knows an alternative?
Regarding the volume measurement, I´m still trying to separate my
particle of interest from other stuff (a cell) in a confocal stack in
order to do particle analysis to calculate volume (the particle and the
cells have almost the same fluorescence intensity in the same channel
and are in contact in some regions). Watershed2D or 3D doesn´t work
beacause of under or oversegmentation as Johannes said. I´ve tryied out
other segmentation plugins but they don´t select what I want. May be
SegmentationAssistant plugin may work but it doesn´t retrieves any roi
and get stucked as soon as I try to change any parameter. The java that
is needed for this plugin (as is pointed out in the plugin webpage) is
no longer available, also. Is there any other alternative to my problem,
perhaps through 3Dreconstruction?.
Any idea will be very belcome, thanks
Paola

[Gabriel Landini]

On Thursday 30 July 2009  09:28:13 Paola Lepanto wrote:
> I´ve been stuck with some problems: regarding the computer memory
> problems, JRockit JMV is no longer available to extend the memory that
> ImageJ can use in 32bits Windows, anybody knows an alternative?

This is probably not what you want to hear, but a free alternative would be to
install some 64 bit linux distribution.

Johannes Schindelin produced a live kubuntu distribution iso file with fiji
that you could put in a usb stick and boot from it to see if that would work
for you before deciding to install to the hard drive. (not sure if that was 32
or 64 bits, though).

Cheers

Gabriel

[Joachim Wesner]

Hi list,

I would like to create a modified FloatProcessor that has uses some special
nonlinear mapping in the Create8BitImage method without touching the
original pixel data.

I´m a little bit confused how to acchieve this, because:

+ Create8BitImage is a "private" method with default/package access rights,
so it cannot be overriden, if the new file is not also a part of the
package "ij.process".

+ I will also likely need to have acces to some other internal data of the
FloatProcessor to do what I plan.

+ Even if I solve this in a brute force way by copying the whole source
code into a new file, the packaging problem remains, which poses a more
general question:

How does one "on the fly" extend a package, if the package itself is still
compressed in a jar? (ij.jar in my case)? Can I keep the new source code in
a private directory
and simply "claim" that it´s part of "ij.process" eg. Or would I need to
(partly) unpack the relevant files? Where exactly would I need to put the
"ij.process" files?

Sorry if these are silly questions, but the docs I find always seem to
assume that I have all the package files ready in the "right" locations.

Mit freundlichen Grüßen / Best regards

Joachim Wesner

Leica Microsystems CMS GmbH | GmbH mit Sitz in Wetzlar | Amtsgericht
Wetzlar  HRB 2432
Geschäftsführer:  Dr. Stefan Traeger | Dr. Wolf-Otto Reuter | Dr. David Roy
Martyr | Colin Davis
www.leica-microsystems.com


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[dscho]

Hi,

On Fri, 31 Jul 2009, Gabriel Landini wrote:

> On Thursday 30 July 2009  09:28:13 Paola Lepanto wrote:
> > I´ve been stuck with some problems: regarding the computer memory
> > problems, JRockit JMV is no longer available to extend the memory that
> > ImageJ can use in 32bits Windows, anybody knows an alternative?
>
> This is probably not what you want to hear, but a free alternative would
> be to install some 64 bit linux distribution.
>
> Johannes Schindelin produced a live kubuntu distribution iso file with
> fiji that you could put in a usb stick and boot from it to see if that
> would work for you before deciding to install to the hard drive. (not
> sure if that was 32 or 64 bits, though).

It is 32-bit for the moment, but I could be talked into providing a 64-bit
version -- after a well-needed week off.

Ciao,
Dscho

[Paola Lepanto]

Hi everyone
Now I´m trying to do a macro using (of course) macro recorder. I would
like to use stack Z-projection plugin using the run() function but I
would need it to allow me to set the range of slices to project for each
stack while running the macro. I know there´s the built-in function:
Macro.getOption, but I couldn´t find it (I´ve updated ImageJ recently).
Is there any alternative or somewhere to download it from? Also if you
can give me some little help about how to call this function in relation
to Z projection plugin, it would be great.
Thanks in advance
Paola

[dpoburko]

Paola Lepanto wrote:

> Hi everyone
> Now I´m trying to do a macro using (of course) macro recorder. I would
> like to use stack Z-projection plugin using the run() function but I
> would need it to allow me to set the range of slices to project for each
> stack while running the macro. I know there´s the built-in function:
> Macro.getOption, but I couldn´t find it (I´ve updated ImageJ recently).
> Is there any alternative or somewhere to download it from? Also if you
> can give me some little help about how to call this function in relation
> to Z projection plugin, it would be great.
> Thanks in advance
> Paola

Hi Paola,

  If I understand your problem ,you simply need a way to run a
Z-projection, where the first and last image are somehow dynamically set.

Here is an example:

//first slice
A = 0;    
//nslices give you the number of slices, whereas the "slice
number/position will be numbered starting at zero
B = nslices()-1;  

run("Z Project...", "start="+ A +" stop=" + B + " projection=[Average
Intensity]");

Alternatively, you could create simple dialogue box to input the values
for A and B (see the dialog box Macro example
http://rsb.info.nih.gov/ij/macros/DialogDemo.txt )

Cheers,
Damon

[Gabriel Landini]

On Monday 03 August 2009, Damon Poburko wrote:

>   If I understand your problem ,you simply need a way to run a
> Z-projection, where the first and last image are somehow dynamically set.
>
> Here is an example:
>
> //first slice
> A = 0;
> //nslices give you the number of slices, whereas the "slice
> number/position will be numbered starting at zero
> B = nslices()-1;
>
> run("Z Project...", "start="+ A +" stop=" + B + " projection=[Average
> Intensity]");

I think that slices start at "1" and end at "nSlices".

G.

[dpoburko]

Gabriel Landini wrote:

> On Monday 03 August 2009, Damon Poburko wrote:
>  
>>   If I understand your problem ,you simply need a way to run a
>> Z-projection, where the first and last image are somehow dynamically set.
>>
>> Here is an example:
>>
>> //first slice
>> A = 0;
>> //nslices give you the number of slices, whereas the "slice
>> number/position will be numbered starting at zero
>> B = nslices()-1;
>>
>> run("Z Project...", "start="+ A +" stop=" + B + " projection=[Average
>> Intensity]");
>>    
>
> I think that slices start at "1" and end at "nSlices".
>
> G.
>  

Thanks for the correction Gabriel. I must have been a little off when
writing this.

Cheers,
Damon

[Paola Lepanto]

Damon Poburko escribió:

> Gabriel Landini wrote:
>> On Monday 03 August 2009, Damon Poburko wrote:
>>  
>>>   If I understand your problem ,you simply need a way to run a
>>> Z-projection, where the first and last image are somehow dynamically
>>> set.
>>>
>>> Here is an example:
>>>
>>> //first slice
>>> A = 0;
>>> //nslices give you the number of slices, whereas the "slice
>>> number/position will be numbered starting at zero
>>> B = nslices()-1;
>>>
>>> run("Z Project...", "start="+ A +" stop=" + B + " projection=[Average
>>> Intensity]");
>>>    
>>
>> I think that slices start at "1" and end at "nSlices".
>>
>> G.
>>  
> Thanks for the correction Gabriel. I must have been a little off when
> writing this.
>
> Cheers,
> Damon

Thank you, but I couldn´t make it work through the way you showed me: it
makes a Z proyection  from the whole stack. What I would like to do is
to select in each image the range of slices to make the projection. So I
tried to  make this other macro that  fails to recognize A as the number
(a pop up says that it expects a numeric value for "Stop") I put in the
dialog box. Am I using the correct functions?, perhaps you can help me:

Dialog.create("Z projection stop");
Dialog.addNumber("Stop:", 30);
Dialog.show();
A = Dialog.getNumber();
run("Z Project...", "start=1 stop=+A+ projection=[Average Intensity]");

Thank you again,
Paola

[dpoburko]

Paola Lepanto wrote:

> Damon Poburko escribió:
>> Gabriel Landini wrote:
>>> On Monday 03 August 2009, Damon Poburko wrote:
>>>  
>>>>   If I understand your problem ,you simply need a way to run a
>>>> Z-projection, where the first and last image are somehow
>>>> dynamically set.
>>>>
>>>> Here is an example:
>>>>
>>>> //first slice
>>>> A = 0;
>>>> //nslices give you the number of slices, whereas the "slice
>>>> number/position will be numbered starting at zero
>>>> B = nslices()-1;
>>>>
>>>> run("Z Project...", "start="+ A +" stop=" + B + " projection=[Average
>>>> Intensity]");
>>>>    
>>>
>>> I think that slices start at "1" and end at "nSlices".
>>>
>>> G.
>>>  
>> Thanks for the correction Gabriel. I must have been a little off when
>> writing this.
>>
>> Cheers,
>> Damon
> Thank you, but I couldn´t make it work through the way you showed me:
> it makes a Z proyection  from the whole stack. What I would like to do
> is to select in each image the range of slices to make the projection.
> So I tried to  make this other macro that  fails to recognize A as the
> number (a pop up says that it expects a numeric value for "Stop") I
> put in the dialog box. Am I using the correct functions?, perhaps you
> can help me:
>
> Dialog.create("Z projection stop");
> Dialog.addNumber("Stop:", 30);
> Dialog.show();
> A = Dialog.getNumber();
> run("Z Project...", "start=1 stop=+A+ projection=[Average Intensity]");
>
> Thank you again,
> Paola

Hi Paolo,

You are 98% there. This should do it.
run("Z Project...", "start=1 stop=" + A + " projection=[Average
Intensity]");

Notice the extra quotation marks. When you interrupt anything in
quotations to introduce a variable, be sure to add the extra quotations
on either side of the pluses so that you have discrete bits of STRING
flanking your + variable +.
For examples,
A = 10;
print("I would like " + A + " donuts.");
// this will print "I would like 10 donuts"

print("I would like + A + donuts.");
// this will print "I would like + A + donuts", which won't make sense
in terms of code.

Cheers,
Damon