MTrack2

[Aryeh Weiss]

I found that if I segment my objects with black background checkbox enabled,
then MTrack2 will fail, since it assumes that the objects are black. (Thanks to
the author Nico Stuurman for helping me to find the problem).
Nico noted that MTrack2 uses ImageJ's particle recognition functions, and
suggested that I ask the mailing list if it is possible to make them recognize
white particles on a black background.

It is not a critical thing, because I can always invert my segmented images to
present black objects (and I can probably use an inverting LUT if it really
bothers me), but I was wondering if this behavior is selectable as an option.

I tried setting white as foreground and black as background in
edit>options>colors...  but that does not seem to do it.

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

Ph:  972-3-5317638
FAX: [phone]

Israel Society for Microscopy 2009 meeting website:
http://materials.technion.ac.il/ism/ISM2009.html

[Gabriel Landini]

> I tried setting white as foreground and black as background in
> edit>options>colors...  but that does not seem to do it.
>
aryeh:
I also use white particles on a black background by default for all the things
I do, but never used MTrack2.

Have a look into this ridiculously long titled link:

http://imagejdocu.tudor.lu/doku.php?id=faq:technical:how_do_i_set_up_imagej_to_deal_with_white_particles_on_a_black_background_by_default

You perhaps need to also select the binary options (explained in the page
above).
I hope it helps,

Gabriel

[Aryeh Weiss]

Gabriel Landini wrote:

>> I tried setting white as foreground and black as background in
>> edit>options>colors...  but that does not seem to do it.
>>
> aryeh:
> I also use white particles on a black background by default for all the things
> I do, but never used MTrack2.
>
> Have a look into this ridiculously long titled link:
>
> http://imagejdocu.tudor.lu/doku.php?id=faq:technical:how_do_i_set_up_imagej_to_deal_with_white_particles_on_a_black_background_by_default
>
> You perhaps need to also select the binary options (explained in the page
> above).
> I hope it helps,
>
> Gabriel
>
>

Thank you for your quick reply. I tried this -- it appears to be equivalent
to selecting the dark background checkbox during apply threshold.
However, MTrack2 still fails in this case.

The interesting thing is that if I use the black background option, then MTrack2
fails, but if I then invert the LUT, them MTrack2 works. One would think that
the LUT should play no role, because the image values do not change.

Essentially, I can have two images that are identical, except that one displays
255 and black and 0 as white, while one displays 255 as white and 0 as black,
and get two different results. That is strange.

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

Ph:  972-3-5317638
FAX: [phone]

Israel Society for Microscopy 2009 meeting website:
http://materials.technion.ac.il/ism/ISM2009.html

[Gabriel Landini]

On Friday 01 May 2009 05:00:31 Aryeh Weiss wrote:
> Thank you for your quick reply. I tried this -- it appears to be equivalent
> to selecting the dark background checkbox during apply threshold.

No. That option will also affect all other binary operations too.
(otherwise dilate and erode, etc are inverted).

> However, MTrack2 still fails in this case.

I see, well, it was worth a try.

> The interesting thing is that if I use the black background option, then
> MTrack2 fails, but if I then invert the LUT, them MTrack2 works. One would
> think that the LUT should play no role, because the image values do not
> change.

Yes, I see the inverted LUT as a source of eternal confusion.
>
> Essentially, I can have two images that are identical, except that one
> displays 255 and black and 0 as white, while one displays 255 as white and
> 0 as black, and get two different results. That is strange.

As I said above...

Cheers,

Gabriel

[Aryeh Weiss]

ok -- I can live with black objects. MTrack2 is very nice -- thank you Nico.

So I decided to try ToAST (because it's there...)
and here is what I got:

java.lang.NullPointerException
        at java.io.File.<init>(File.java:262)
        at ToAST25_.track(ToAST25_.java:368)
        at ToAST25_.run(ToAST25_.java:151)
        at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:245)
        at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:102)
        at ij.IJ.runUserPlugIn(IJ.java:183)
        at ij.IJ.runPlugIn(IJ.java:147)
        at ij.Executer.runCommand(Executer.java:143)
        at ij.Executer.run(Executer.java:75)
        at java.lang.Thread.run(Thread.java:619)

This is happening on the latest Fiji distribution. Although I usually run Fiji
with the latest ij.jar and the JRockit JRE, this time I am using the latest
stock Fiji distribution, to rule out my JRE as a source of the problem.

The error occurs with options checked, but also with all of the options
unchecked. Input is a binary file -- the very one that MTrack2 processes with no
problem.

I am not sure if this is a Fiji issue or an ImageJ issue, so I am posting here.
I apologize in advance if it should have been posted elsewhere, but I assume
that all of the Fiji people also read this list (Fiji is just ImageJ...).

Any ideas?
--aryeh

Gabriel Landini wrote:

> On Friday 01 May 2009 05:00:31 Aryeh Weiss wrote:
>> Thank you for your quick reply. I tried this -- it appears to be equivalent
>> to selecting the dark background checkbox during apply threshold.
>
> No. That option will also affect all other binary operations too.
> (otherwise dilate and erode, etc are inverted).
>
>> However, MTrack2 still fails in this case.
>
> I see, well, it was worth a try.
>
>> The interesting thing is that if I use the black background option, then
>> MTrack2 fails, but if I then invert the LUT, them MTrack2 works. One would
>> think that the LUT should play no role, because the image values do not
>> change.
>
> Yes, I see the inverted LUT as a source of eternal confusion.
>> Essentially, I can have two images that are identical, except that one
>> displays 255 and black and 0 as white, while one displays 255 as white and
>> 0 as black, and get two different results. That is strange.
>
> As I said above...
>
> Cheers,
>
> Gabriel
>
>

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

Ph:  972-3-5317638
FAX: [phone]

Israel Society for Microscopy 2009 meeting website:
http://materials.technion.ac.il/ism/ISM2009.html