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Fourier Ring Correlation Plugin

30 bytes removed, 08:01, 8 July 2018
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== Purpose ==
Making use of the Fourier Ring Correlation Implementation by Alex Herbert
which is itself adapted from the FIRE (Fourier Image REsolution) plugin produced as part of the paper
'''Niewenhuizen, et al (2013). Measuring image resolution in optical nanoscopy. Nature Methods, 10, 557''' <ref>{{Cite journal| issn = 1548-7091| volume = 10| issue = 6| pages = 557–562| last1 = Nieuwenhuizen| first1 = Robert P J| last2 = Lidke| first2 = Keith A| last3 = Bates| first3 = Mark| last4 = Puig| first4 = Daniela Leyton| last5 = Grunwald| first5 = David| last6 = Stallinga| first6 = Sjoerd| last7 = Rieger| first7 = Bernd| title = Measuring image resolution in optical nanoscopy| journal = Nat Meth| date = 2013-06}}</ref>
 
== Details ==
=== Threshold Methods ===
 
There are three threshold methods currently implemented
# '''Fixed 1/7''': Finds the FIRE number when the FRC curve reaches a correlation value of 1/7.
# '''Half-bit''': Threshold method where the intersection of the threshold curve with the FRC defines the point where there is 1/2 bit of information per pixel.
# '''Three sigma''': The intersection of the FRC curve with this threshold defines the value where the FRC begins primarily representing high frequency noise.
 
Please see the publication '''van Hell and Schatz, Fourier shell correlation threshold criteria, Journal of Structural Biology 151, 2005'''<ref>{{Cite journal| doi = 10.1016/j.jsb.2005.05.009| issn = 1047-8477| volume = 151| issue = 3| pages = 250–262| last1 = van Heel| first1 = Marin| last2 = Schatz| first2 = Michael| title = Fourier shell correlation threshold criteria| journal = Journal of Structural Biology| date = 2005-09}}</ref> for more information on the calculation of these criteria.
= Updates =
If you are using FRC to compare different images or conditions, and your images do not change size, then the relative differences are still perfectly valid, but absolute values might be off.
=Purpose =Making use of the Fourier Ring Correlation Implementation by Alex Herbertwhich is itself adapted from the FIRE (Fourier Image REsolution) plugin produced as part of the paper'''Niewenhuizen, et al (2013). Measuring image resolution in optical nanoscopy. Nature Methods, 10, 557''' <ref>{{Cite journal| issn = 1548-7091| volume = 10| issue = 6| pages = 557–562| last1 = Nieuwenhuizen| first1 = Robert P J| last2 = Lidke| first2 = Keith A| last3 = Bates| first3 = Mark| last4 = Puig| first4 = Daniela Leyton| last5 = Grunwald| first5 = David| last6 = Stallinga| first6 = Sjoerd| last7 = Rieger| first7 = Bernd| title = Measuring image resolution in optical nanoscopy| journal = Nat Meth| date = 2013-06}}</ref> = Details === Threshold Methods ==There are three threshold methods currently implemented# '''Fixed 1/7''': Finds the FIRE number when the FRC curve reaches a correlation value of 1/7.# '''Half-bit''': Threshold method where the intersection of the threshold curve with the FRC defines the point where there is 1/2 bit of information per pixel. # '''Three sigma''': The intersection of the FRC curve with this threshold defines the value where the FRC begins primarily representing high frequency noise. Please see the publication '''van Hell and Schatz, Fourier shell correlation threshold criteria, Journal of Structural Biology 151, 2005'''<ref>{{Cite journal| doi = 10.1016/j.jsb.2005.05.009| issn = 1047-8477| volume = 151| issue = 3| pages = 250–262| last1 = van Heel| first1 = Marin| last2 = Schatz| first2 = Michael| title = Fourier shell correlation threshold criteria| journal = Journal of Structural Biology| date = 2005-09}}</ref> for more information on the calculation of these criteria.  == Image Calibration ===
We recommend you use a calibrated image so that your results are in calibrated units (microns, millimeters, etc..) directly. The plugin will always return both the non calibrated values and the calibrated ones as separate columns.
== Installation ==
This plugin is available from the [[List of update sites|BIOP Update Site]]
This places it in a "BIOP" Folder in the plugins directory of Fiji/ImageJ
== Use ==
=== Direct Use ===
[[File:frc-dialog-std.png |500px|thumb|right|Plugin Dialog choices Standard Use]]
You need two images open to perform the FRC.
=== Batch Mode ===
[[File:Frc-dialog-batch.png |500px|thumb|right|Plugin Dialog choices in Batch mode]]
The plugin will open one folder, and perform the FRC for each image that has an image in the second folder '''with the same name'''.
=== Results ===
The plugin writes the FIRE (Fourier Image REsolution) number on a Results Table that gets appended as the plugin gets used. The column name reflects the calibration of the image and the threshold method selected.
=== Plots ===
The Plugin can display a plot of the FRC curve, along with the LOESS smoothed version of the curve. Finally it displays the threshold method used and the intersection of the FRC with the threshold, providing the FIRE number. The X dimension is in the frequency domain and represents pixels<sup>-1</sup>
In the case of batch processing, if ''Save Plot'' is checked, the plugin creates a new folder in the parent directory called "Graphs" and saves an over-sampled plot with the name of the image and threshold method.
== Macro Recordable ==
Making use of the GenericDialog class, the plugin is macro-recordable. An example is shown below
<source lang="java">
</source>
== Running from a Plugin ==
If you would like to use the FRC class in your own plugin, you can either use the one from Alex Herbert on [https://github.com/aherbert/GDSC-SMLM GitHub] if you're already using his excellent SMLM plugins. Otherwise you can use the one that was re-purposed here through the following import
There are other methods to get the FRC curve, see the [https://c4science.ch/diffusion/988/browse/master/src/main/java/ch/epfl/biop/frc/FRC.java FRC.java file], which was very well documented.
== Notes ==
[[Category:Plugins]]
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