rbnvrw
commented
4 years ago Hi @komodovaran, I'm assuming your using the locate or batch function of Trackpy.
From the documentation (see http://soft-matter.github.io/trackpy/v0.4.2/generated/trackpy.locate.html#trackpy.locate):
Preprocess the image by performing a band pass and a threshold.
This is the only preprocessing that is done as far as I know and it can be controlled using the smoothing_size and threshold keywords.
If you need to do other background corrections, you can implement these yourself using Pipelines (see for example http://soft-matter.github.io/pims/v0.4.1/pipelines.html)
I hope this helps!
I couldn't find anything about it in the docs, so now I'll ask here.
Take an image like this for example:
There's a higher background near the center (because they're fluorescent particles inside a cell), and the background will also vary depending on the "bleed" from a high local concentration.
How does TrackPy deal with this? The intensity "mass" sounds like just integrating everything inside a circle.
What I'm currently doing is using the track coordinates to draw adjustable masks for each frame to get signal and local background and subtract that. Am I better or worse off by doing this? TrackPy intensities just seem way noisier.