Obtain EF values in Ellipsoid Factor

Image Analysis
#1

Hello,

I am only able to obtain EF values via histogram where the count is on a pixel-by-pixel basis. I would like to obtain a table of EF values on an ellipsoid-by-ellipsoid basis for statistical analysis - in other words, the a/b and b/c values used to generate the Flynn plot.

I am able get an analogous set of values from the Flynn plot image itself by using the Analyze Particles function (inverting y coordinates, setting particle size range to match the plot circles, copy-pasting x-y coordinates into Excel, normalizing coordinate values to 1024x1024 pixels, calculating y-x). However, this is far too labor intensive given the number of samples I have. It also excludes data where the points overlap on the plot (as they are of a different size and shape).

Can the plugin be modified to include an output of the data used to generate the Flynn plot?

Thank you!

1 Like
#2

This is one for @alessandrofelder.

@jwatt3 : we’d have to clarify exactly what you need. I don’t remember off the top of my head whether the points on the Flynn plot are volume weighted (big ellipsoids have higher values). You can make the points sharper by reducing the Gaussian blur to 0.

It’s potentially possible to output the list of ellipsoids, or to access them via the code’s API, or just dump the full list (can be very long) of a, b, and c values, by ellipsoid, to the log. Something that you lose by doing an ellipsoid-by-ellipsoid analysis is the winner-takes-all overlapping. Many ellipsoids and their regions are not used in the final result because they are overlapped by larger ellipsoids.

Please come back to us with what exactly you need and what you need it for so we can decide how best to help.

1 Like
#3

Yup, happy to help @jwatt3.
Would you need a/b and b/c values for each foreground pixel or for each ellipsoid?
The data can be big, as @mdoube points out.