This list of frequently asked questions is compiled from several questions we have seen several times on the ImageJ forum. It will be updated as questions appear there.
- 1 Limitations of TrackMate for spot detection.
- 2 Exporting TrackMate spots to ImageJ1 ROIs.
- 3 Copying TrackMate tracking data to another image file.
- 4 Exporting TrakMate overlay to a movie.
- 5 Customizing the look of tracks during movie export.
- 6 Various java.lang.NoClassDefFoundErrors upon execution.
Limitations of TrackMate for spot detection.
We are using TrackMate to generate lineages of X cells in live Y and are interested in how the intensity of a signal of interest changes over time, but also in the cell volume. Since most of our cells are not spherical and some are clustered close together, the LoG detector yields rather unsatisfying results. Is it possible to detect these cells based on their actual shape instead of assuming they are all spheres and measure the volume of such segmented cells?
You are looking for segmentation algorithm, that can return the contour of an object, and harness complex object shapes. TrackMate just ships detection algorithms, that only return the X,Y,Z coordinates of each blob.
As of today, there are no plans we are aware of to make TrackMate ship segmentation algorithms.
Exporting TrackMate spots to ImageJ1 ROIs.
TrackMate found my particles, and the preview function is usefeul. However I can't seem to figure out how to export all the TrackMate overlays to individual ROIs, so that I can analyse them with other plugins.
There is a ROI exporter action is in a separate package called TrackMate-extras. To install it, you have to download its jar file and drop it in the plugins folder of Fiji. Link and instructions are on the TrackMate#Downloadable_jars page.
An action called Export current spots to IJ rois will appear in the menu of the action panel (the very last one in the GUI). It will convert each spot to a point in the Multi-Point ROI tool of ImageJ1.
Copying TrackMate tracking data to another image file.
We would like to know if there is any tool to copy the spots/track created in one stack (fluorophore 1, file 1) and paste them in another stack (fluorophore 2, file 2). We explored the option Copy overlay to but it did not work for more than a single frame of the stack.
The simplest solution consists in editing the TrackMate XML file, and have it point to another tif file.
- Make a copy of the XML file, and edit it in a good text editor;
- Find in the XML file the line that points to the TIF file on which you did the analysis. It looks like this:
<Settings> <ImageData filename="DUP_TIM1 GFP clat dsred TIRF-5.tif" folder="/Users/tinevez/Desktop/" width="310" height="362" nslices="1" nframes="113" pixelwidth="0.1" pixelheight="0.1" voxeldepth="1.0" timeinterval="2.463" />
- Change the filename tag to point to the other TIF file on which you want to copy the overlay.
- Next time you open the edited file in TrackMate, it will also open the new TIF file and put the annotation on it.
Exporting TrakMate overlay to a movie.
In TrackMate after completing tracking, is there any way to export/save a movie with all tracks and moving spots (exactly as it appears after using the TrackMate)?
If you keep clicking on the Next button on the GUI, you will reach the last panel of the GUI, which collects miscellaneous actions.
One of them is called Capture TrackMate overlay and does what you need. It generates a RGB stack with the tracks burned-in. After that you have to export the stack to AVI and you are done.
Careful: the frame capture is simple and brutal. If you have something that passes over the TrackMate viewer while the capture is going on, it will be captured in the final movie.
Customizing the look of tracks during movie export.
I am aware of Capture TrackMate overlay function but it only provides the final picture of the track(s) overlayed on the moving particle. I'm interested in showing that the tracks are (or a single track) being formed as the particles move.
The overlay capture abides to the display settings you set in the Display Settings GUI panel. By changing the Track display mode here, you can get what you need. For instance choosing the Show local tracks, backward will generate a "dragon tail" aspect for the tracks in the movie.
Various java.lang.NoClassDefFoundErrors upon execution.
These errors may popup when you try to launch TrackMate, or plot features. A stack trace will show in the console and the second line will resemble this:
Exception in thread "TrackMate plot spot features thread" java.lang.NoClassDefFoundError: com/itextpdf/text/DocumentException at fiji.plugin.trackmate.features.SpotFeatureGrapher.render(SpotFeatureGrapher.java:115) at fiji.plugin.trackmate.gui.GrapherPanel.plotSpotFeatures(GrapherPanel.java:189) at fiji.plugin.trackmate.gui.GrapherPanel.access$100(GrapherPanel.java ...
This kind of error is caused when a Java class is missing in your installation. In most cases, this happens because your Fiji installation did not update properly. Possible solutions are