Ggood afternoon,
I’m trying to analyze bright field videos with trackmate. I have to follow some cells but It seems that the cells (bright field) have a brighter halo, and that white halo is what the Trackmate follows. As much as I try to change contrast, color, etc., I do not get the Trackmate to follow the cell instead of the halo.
Could someone help me??
Thanks so much!!
Hi @adiaz
Normally TrackMate only ships detectors made for fluorescence images.
However we have had some success in the past with phase-contrast images that can be generalized maybe to bright field images.
Try to invert the image so that the halo around the cell is dark. Set the LoG detector diameter to the diameter of this halo. This might work,
best
jy
Good afternoon,
I’m going to try it, thank you very much!!
Regards,
Adiaz
Good morning,
Thank you very much for the help Jy, but I still have the same problem. I
n the previous situation It was following the brighter halo and now inverting the colors the darkest. I have also changed the diameter of the detector … What do you think I could do?
Thank you
Hi @adiaz,
you might want to try to apply a Variance filter ►Process►Filter►Variance… on your images. This should give you a fluorescent-like image appearance and might improve detection quality in TrackMate.
This will reduce the “shadowing” effect of the halos around your cells and therefore it lets them appear more uniform.
Hope this helps
Hi @adiaz
I don’t think the existing detectors can do better than what you have now.
As @biovoxxel suggested you will have to transform it somehow to make it look like a fluorescence image, where cells are bight over black background.
Good afternoon,
I will try to transform it.
Thank you very much to both of you for your help!!
Best,
ADiaz