0000052: glyphs / circular statistics for Orientation lines

OpenPolScope MantisBT - Orientation Lines V4

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0000052

Orientation Lines V4

[All Projects] enhancement

public

2013-08-02 18:43

2013-08-02 18:44

Reporter

admin

Assigned To

grant

Priority

urgent

Severity

feature

Reproducibility

have not tried

Status

assigned

Resolution

open

Platform

OS Version

Product Version

[OpenPolScope-API] 2.15

Target Version

[OpenPolScope-API] 2.16

Fixed in Version

Summary

0000052: glyphs / circular statistics for Orientation lines

Description

add glyphs / circular statistics / additions from Grant/Rudolf/Hannah's code

Added by Shalin:

We have been using Pol-Analyzer for exploring data taken in
collaboration with Clare Waterman's group (mostly real-time PolScope
data converted to MM format) and with Daniel Gerlich (Nikon PolScope).

In both cases, we need to compare average anisotropy/orientation in
following ways:
a) When the lines are plotted every Nth pixel, it is expected that
intensity is averaged over NXN pixels before the
anisotropy/orientation are calculated and plotted. We can plot the
orientation line at the center of NXN pixels.
b) Often times the biologically interesting measurement is to compare
net anisotropy over manually selected regions. We would like to draw a
ROI manually and obtain anisotropy/orientation using intensities
averaged over that ROI.
c) An extension of b) for rectangular ROI is that the ROI can be
partitioned into rows and columns with anisotropy/orientation obtained
over each sub-ROI (the mode that Rudolf implemented with ROI averages
with Lines V1).

For b) and c) an option to plot orientation fan (displaying average
orientation and its variance as Grant has implemented) will be quite
informative.

It seems that a) is properly implemented within current Azim Lines
plugin as an option.

It seems that b) and c) can be made by combining Rudolf's plugin and
Grant's orientation fan. If we can bump these feature requests higher
in priority, they can receive good use and testing over next few
weeks.

Also, it is important to be able to export the values, for example by
pushing them to the measurement window of ImageJ.

Steps To Reproduce

Additional Information

moved from Orientation Lines V3 project (Issue 0000024)