Trackmate for Windows7

[Marcia Yoshida]

Dear sirs.

I am new in Fiji and I have been trying to go through the TrackMate tutorial at home (ver. 2.2.0 64-bit my pc has a windows 7 os) but cannot complete the tracking after choosing the LAP tracker settings (for both the simple LAP and the not-so-simple LAP trackers).



When I click 'next', the panel goes back to setting parameters and resets all of them to 0 or some other number (like in the picture). It seems to work fine in windows xp though. Is there something else I should do before running the program in windows7?

I am terribly, terribly sorry for my noobiness if this is something too trivial.
Thank you very much,
Marcia

[dscho]

Hi Marcia,

On Thu, 27 Mar 2014, Marcia Yoshida wrote:

> I am new in Fiji and I have been trying to go through the TrackMate tutorial
> at home (ver. 2.2.0 64-bit my pc has a windows 7 os) but cannot complete the
> tracking after choosing the LAP tracker settings (for both the simple LAP
> and the not-so-simple LAP trackers).
>
> <http://imagej.1557.x6.nabble.com/file/n5007108/lapbug.png>
>
> When I click 'next', the panel goes back to setting parameters and resets
> all of them to 0 or some other number (like in the picture).

Could you follow the steps outlined in
http://fiji.sc/Debugging#Command_line_debugging to catch the console
output? Hopefully there will be more clues.

Ciao,
Johannes

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[dscho]

Hi Marcia,

On Fri, 28 Mar 2014, Johannes Schindelin wrote:

> On Thu, 27 Mar 2014, Marcia Yoshida wrote:
>
> > I am new in Fiji and I have been trying to go through the TrackMate
> > tutorial at home (ver. 2.2.0 64-bit my pc has a windows 7 os) but
> > cannot complete the tracking after choosing the LAP tracker settings
> > (for both the simple LAP and the not-so-simple LAP trackers).
> >
> > <http://imagej.1557.x6.nabble.com/file/n5007108/lapbug.png>
> >
> > When I click 'next', the panel goes back to setting parameters and
> > resets all of them to 0 or some other number (like in the picture).
>
> Could you follow the steps outlined in
> http://fiji.sc/Debugging#Command_line_debugging to catch the console
> output? Hopefully there will be more clues.

Actually, I have some hopefully helpful advice even without the console
output: I just realized that the max distance is set to 0 for both frame
linking and gap closing. That is most likely not what you want.

Keep in mind that the idea is to link objects (e.g. cells) that were
detected in individual frames so that you get a track over time. In the
following, I will often use the term "cell" or even "vesicle" as a synonym
for "object".

The "max distance" setting in the frame linking section lets you limit how
far a cell is supposed to travel *at most* between two frames. If you
limit this to 0, only tracks are allowed with absolutely stationary cells,
something that is almost certain never to happen.

I seem to recall that the default setting is 15 pixels. Why don't you give
that a try?

The max distance in the gap closing is similar to the other max distance
in spirit, but only kicks in when closing gaps on the time axis. Imagine
e.g. a study using TIRF microscopy, where vesicles drop out of the focal
plane from time to time. Often, it is still possible to track the vesicles
because they are only gone for a couple of frames. Gap closing to the
rescue! The "max frame gap" setting says how many frames an object can be
missing before we refuse to connect tracks before and after the missing
frames. And the "max distance" setting is exactly the same as before,
except that we want to limit the total distance an object could possibly
have traveled during those missing frames and still be considered the same
object. Therefore, this 'max distance' setting most likely needs to be
even larger than the one above if you want to allow cells to be missing
from five consecutive frames.

Hopefully that helps,
Johannes

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[Marcia Yoshida]

Dear Mr. Schindelin,

thank you very much for your quick reply!

Johannes Schindelin wrote

I just realized that the max distance is set to 0 for both frame
linking and gap closing.

I am sorry I was not clear in my first post; I did try using the default settings for both 'frame linking' and 'gap closing', but when I clicked the 'next' button, the panel just seemed to erase  those settings to zero and disabled the 'next' button (that's what the picture shows).

When analysing one of my own videos (for which, btw, spot detecting and filtering has worked amazingly well! I need to congratulate youse for the easy-to-follow tutorials and dummy-friendly user interface!), I tried changing max distance for up to 200 pixels (I tried several values) but again the panel reset them to zero, disabled the 'next' button and wouldn't let me go on with tracking.

It is hard to explain exactly what happened without writing too much, so I made the mistake of writing too little. I posted a bug report on bugzilla (bug number 723) and also I will try catching the console output.
Again, thank you very much!

[dscho]

Hi Marcia,

On Thu, 27 Mar 2014, Marcia Yoshida wrote:

> Johannes Schindelin wrote
> > I just realized that the max distance is set to 0 for both frame
> > linking and gap closing.
>
> I am sorry I was not clear in my first post; I did try using the default
> settings for both 'frame linking' and 'gap closing', but when I clicked the
> 'next' button, the panel just seemed to erase  those settings to zero and
> disabled the 'next' button (that's what the picture shows).

Please note that it can take quite a long time to perform that linking
step. IIRC there is some progress bar in the top of the GUI that might
take some time to start up.

You should also be able to see that TrackMate is using a lot of horse
power in your Windows' Task Manager.

We always wanted to add a faster linking step there, and it is still
planned, it's just that I had to tend to other, pressing projects.

Ciao,
Johannes

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