TrackMate track viewer in Napari

Announcements
, , ,
#1

Hello, A new viewer for TrackMate tracks has been released today. I made it in Napari for viewing 3D + time tracks for dividing and non-dividing cells. The tracks are selected one at a time and track information is plotted dynamically in the widget popping inline next to the napari track viewer. I used track layer of napari to display the tracks and animation tool to save the track as an mp4 along the user chosen view.

I made this for the specific project that I am working on but I think it will be useful for some people as an out of box solution or as a code template for developers to code around it.

Some examples:
https://twitter.com/EntraCod/status/1350259570183176192

https://twitter.com/EntraCod/status/1348829936505778176

9 Likes
#2

Thanks for sharing @kapoorlab.

You might want to try using either of the new hook_specifications we released last week in the 0.4.3 version of napari, napari_experimental_provide_function_widget or napari_experimental_provide_dock_widget.

These would allow you to leverage more of the napari plugin interface and might make it easier to use your tracks viewer alongside other napari tools, see more on plugins here.

4 Likes
#3

Yeah Thanks @sofroniewn, I will give it a go and ask for help if I get stuck somewhere.

1 Like
#4

Hi again @sofroniewn , I have released a new version with code improvements but not made it into a “real” Napari plugin yet just added the QT push buttons, animations , dropdown menu and plots in the napari browser. Its only because am doing many things at the same time so haven’t been able to go over the hook specification or the plugins yet. But if you want to do a PR on my repo it is here:
TM XML export into Napari

1 Like