TrackMate error when loading a saved XML file


#1

Dear Jean-Yves,

I came across a TrackMate error when loading a saved XML file. There are mainly two problems: (1) when I click on the detected spots, the error appears (Figure 1). (2) actually thousands of cells are detected and tracked, but only several cells in the first 4 frames are displayed (no outlines for other cells in Figure 2). I have re-opened this xml file successfully before but not any more. Worse still, I’ve tracked several movies and now all of them have such problems.

Could you please help solve this problem? Many thanks.


#2

Dear @LilyCrystal,

is it possible that your installation of Fiji has changed between saving the XMLs and trying to re-open them?

As far as I know, the Spot intensity per channel analyzer is by default not bundled with TrackMate. You will have to install TrackMate-extras to make that analyzer available. Do you provide an update-site that ships those extras, @tinevez?

Best,
Stefan


#3

Dear @stelfrich,

I see. You are right. The modified TrackMate is missing and it is used for the multi-channel images. As you suggest, after downloading TrackMate-extras, how do I apply it in Fiji? In other words, how to combine it with TrackMate_3.4.2? Thanks a lot.

Best regards,
Liyan


#4

The download “only” provides the sources for the additional analyzers. You can either go into the downloaded folder from the command-line/terminal and use Maven to build it, i.e. mvn package, or you can download a version that I have compiled some minutes ago: https://www.dropbox.com/s/jagc4egv7sul6gc/TrackMate_extras-0.0.3.jar?dl=0

Subsequently, put the generated (or downloaded) *.jar file into /path/to/Fiji.app/jars. After a restart, TrackMate should pick up the additional analyzers.

Best,
Stefan


#5

Dear @stelfrich

Thanks a lot. I’ve downloaded it and no error when I click the outlines. But still there are two problems: 1) Cell outlines in the first 5 frames exist but not for the following ones; 2) When I click the cell in TrackScheme (e.g. frame 2 in Figure 3), it does not go to the corresponding cell in the sliding bar (z-axis in Figure 3). Does it mean that there is something wrong with the saved XML file?

                                           Figure 3

Best regards,
Liyan


#6

Judging from my previous comments, you are not loading the XML file from the same Fiji instance from which the XML file was written? Maybe, you also have updated TrackMate in between? You can check for the TrackMate version that has created the XML file by opening it in a text editor of your choice and looking at the second line in the file:

<?xml version="1.0" encoding="UTF-8"?>
<TrackMate version="3.4.2">
...

While you have the file open, you can also check if you have spots in the frames > 5 by searching for the following tags:

<SpotsInFrame frame="6">
...
</SpotsInFrame>
<SpotsInFrame frame="7">
...
</SpotsInFrame>
...

In general, it is always a good idea to go back to the version that was used to save the XML files.

Best,
Stefan


#7

Dear @stelfrich,

Thanks for your good comments. I’ve tried that as you mentioned. I changed it back to the old version and checked this xml file. I found that all cell information (e.g., size, intensity, frames) is recorded, but still no TrackScheme interface and no cell outlines show from frame 6 onward. Probably I’ll do the experiment again using the new multi-channel TrackMate version. By the way, is there any other way to apply TrackMate-extras in TrackMate? e.g., copy the extra folders into TrackMate and build it again. Does it make sense? Many thanks again.

Best regards,
Liyan


#8

Depending on your experiment, that might be the easiest solution.

For now, TrackMate-extras is a separate module. I assume that @tinevez has made that choice deliberately to keep vanilla TrackMate as easy-to-use and clean as possible. If demand for multi-channel measurements is communicated to him, he might change that in future. Gist: I am not the one to decide :wink:


#9

Hi all,
I am late regarding the proper distribution of 3rd party contributions to TrackMate, and will still do for a couple of weeks…
It is not by design, but just lack of time.


#10

Hi @tinevez and @stelfrich,

Thanks for your help. I understand that it takes time to distribute TrackMate’s new version. Anyway, it works well for the multi-channel images by adding TrackMate-extras when I do the experiments again.

By the way, when I manually add spots in TrackScheme and then link them, is there any way to link some (e.g., 10) consecutive spots once but not one by one? The other question is that if I delete some spots by mistake, how can I recover them in TrackScheme?

Best regards,
Liyan


#11

Dear Jean_Yves,
I have the same issue LilyCrystal described.
I am working on a time lapse stack. I generated xml and reloaded it immediately back to the same Fiji -> TrackMate 3.5.3 with all extras installed, I have a similar problem as LilyCrystal described here. I noticed that the spot size is getting smaller when the frame number increases, and becomes a minimum size and labels were not changed and were all disappeared > 15th frame. Do you have any idea on what I did wrong. Thanks a lot!

Bin


#12

Hi @Bin_XU

This looks like a classical dimensionality problem.
Check the FAQ: https://imagej.net/TrackMate_FAQ#Only_the_first_time-point_of_the_track_is_displayed_after_loading.


#13

Solved. Thanks a lot!

Bin