Trackmate script: calculate mean intensity based on estimated diameter than physical radius

Hi there!
I am working on measuring mean intensity of vesicles from each track. I am aware that Trackmate calculates mean intensity of each track using physical radius, R. But I want to estimate mean intensity based on estimated diameter which is calculated from contrast difference. To do this, I am now trying to write a script in MATLAB or Python. I was wondering if I can edit the Trackmate script to do this task or any other API would do. Any comments or suggestions would be helpful!
Thanks for your time! I am really grateful for your quick responses in my past queries!

John

Hi John

Could you please make this post public so that others can join in the conversation?

Best
Jy

5 Likes

Hi Tinvevez,
I added the user as “imagej” . I assume , the post is now under public display.
John

I don’t think new users can make topics public, so I went ahead and did so, using the wrench :wrench: button available to admins.

2 Likes

Hi @John1

I think there is a simpler way.

In the last panel of TrackMate there is a list of actions that do various things. One of them sets the radius of the spots to be the one calculated by the estimated diameter function.

Then you can recompiute all feature values with the new radius with another action in the same list.

Tell us if it works!

Hi tinevez,
awesome!:clap:
yes, you nailed it. It seems, Trackmate has all possible options that I want. I need to dig through it. I will!
I really appreciate your fast and very helpful response.

John

Thanks!
Can you mark the question as answered?

Good luck with what’s next!