Define pixel size and override radii in FIMTrack v2 csv files
Reconstructed outlines for tracks from FIMTrack v2 table.csv files can be very noisy due to highly variable radii (both in space and time). These radii can be zero or abnormally large.
For visualization purposes, we need to override the radius_1
, radius_2
and radius_3
rows and use constant values instead.
The larvatagger.jl import
command could feature an argument --override="radius_1:<val1>,radius_2:<val2>,radius_3:<val3>"
.
EDIT: as expected, larvae exhibiting torturous shapes seem to be segmentation errors in most cases.
We recycle this issue to mention the introduction of the --pixelsize
argument to larvatagger.jl import
.
Pixel size is passed in micrometers and translates into space coordinates in millimeters.