What Is the Best Way to Track Cell Divisions?


#1

Hi all:

I’m interested in tracking cell lineages, particularly the timing of cell divisions and position of every cell over time. I tried LineageTracker Plugin but I get the following error message:

java.lang.NullPointerException
at util.GenericDataLoader.findPlugins(GenericDataLoader.java:528)
at main.Run_Segmentation.makeSegChoice(Run_Segmentation.java:386)
at main.Run_Segmentation.displayEditWindow(Run_Segmentation.java:322)
at main.Run_Segmentation.run(Run_Segmentation.java:288)
at main.Run_Segmentation.run(Run_Segmentation.java:123)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:662)

Could anyone fix this problem, or suggest some plugins that suit my purpose better? (I’m dealing with large image files, 6000*4000 pixels, if that matters. On an older computer, LineageTracker is able to run, but is very slow and often crashes.)
Thanks a lot!


#2

Hi @Yuchao_Chen

So… I don’t have experience using the LineageTracker plugin you mentioned… but I do know of the tool MaMuT that ships with TrackScheme - should be exactly what you need for lineage tracking. And there is the plugin TrackMate too!. They are definitely worth checking out, and the developer - @tinevez - is active here on the forum as well. :slight_smile:

eta


#3

Thank you so much! I’ll try them out!


#4

If you have more questions @Yuchao_Chen - just post here again on the Forum. We are here to help! :slight_smile:


#5

You might want to try the LineageMapper plugin (available from the update site menu within Fiji).

LineageMapper tracks segmented labeled images so it requires you to pre-segment your cells using another algorithm.

As one of the LineageMapper devs I can assist with any problems you encounter.

-Michael

https://pages.nist.gov/Lineage-Mapper/


#6

Hi Michael: Thanks a lot!