MaMut: Writing additional data to mamut_xml-files



Hi everyone!

I would like to write additional information into the mamut- xml file that I want to use for further analyses of my cell lineage with python. I want to write information on cell generation, identity of sub lineages or simple comments and cell fates into the attributes of the spot objects that are listed in the gamut-generated xml-file.

Trying around a bit I found out that I can add information in the format of key-value pairs (e.g. *cell_generation=„1“ ) to a spot - object. MaMut will still open the file normally.

A problem occurs when I enter information as a string of letters (e.g. fate=„mesoderm“ ). Then FIJI gives an exception when I try to open the file. I also tried adding appropriate entries to the spot features at the beginning of the file and changing the entry for isint from ‚true’ to ‚false‘.

Is there a way for me to write plain text into the spot-objects?
I would be very grateful for any advice.


Hi @jirikowg

This is an interesting question!
Can you copy/paste an example with the error MaMuT gave when you try to open a modified file?


OK. Here´s a copy of the error-message:
(Fiji Is Just) ImageJ 2.0.0-rc-67/1.52d; Java 1.8.0_66 [64-bit]; Mac OS X 10.12.6; 112MB of 6400MB (1%)

java.lang.NumberFormatException: For input string: “wow”
at sun.misc.FloatingDecimal.readJavaFormatString(
at sun.misc.FloatingDecimal.parseDouble(
at java.lang.Double.parseDouble(
at java.lang.Double.valueOf(
at fiji.plugin.mamut.LoadMamutAnnotationPlugin.load(
at ij.IJ.runUserPlugIn(
at ij.IJ.runPlugIn(
at ij.Executer.runCommand(

and I pasted a link to the .xml-file below creating the error message.
When I replace “wow” with “1” in line 47 0f the xml I do not get an error.


Ok so I checked what caused the error, and it turned out like this:
In the loading code, all the attrbutes of a spot in the XML files are transformed into a number:

spot.putFeature( att.getName(), Double.valueOf( att.getValue() ) );

If one of the attribute is not a number, then this line crashes.

I see no solution that would not require a change to TrackMate code. So I want to ask: Do you really need this? Do other people really need this as well?


Hi Jean-Ives,
thanks for checking out the string problem. I was hoping to display user comments from converted SIMI-Biocell lineage data in the text window of track scheme, but it´s not a top priority, so no worries, and thanks again.


Hopefully you will be able to write a Mastodon plugin to make just that.
… when we will release it :slight_smile: