Version v0.3.0 - New name, new features, bugfixes

With this release, Cilility_JNH is renamed to FreQ.

Furthermore, several changes were introduced to allow a more simple handling of the software. These changes are listed below.

Bugfixes

• From this version on, the powers are more accurately calculated as 2*sqrt(real*real+imaginary*imaginary)/(length of the time series), whereas in previous versions powers were calculated as sqrt(real*real+imaginary*imaginary)/(length of the time series) (real and imaginary refer to the real and imaginary outputs of the Fourier transform).
• Now the entire half of the spectrum is plotted in spectra plots. In previous versions the spectra plots' y axis was limited.
• Rename "APC" in output files to the correct abbreviation "APS" (= "assembled power spectrum", which is determined as the average spectrum of the power spectra from all signal pixels (if "extract signal regions" is not selected by the user, all pixels of the image are included)).

News

Make the application of specialized functions customizable via the settings dialog

• Make it optional to remove the power background (which is determined based on low-power pixels in the image):
  

• Make it optional to extract signal regions and allow adjustments of the SD threshold and the range:
  

• Make it optional to determine results in a user-defined region of interest:
  

• Make the output of advanced, complex plots optional. The new version only outputs phase maps and a map for the center-of-mass of the frequency spectrum if the following checkbox is activated in the settings dialog: .

New features

• Output spectra in dB in the main text file.
• Clean and improve layout of main text file.
• Add link to output text files, directing to the GitHub repository.
• Add a help button to the settings dialog - the button directs to the GitHub repository.
• New color map for frequency and power plots:
  
• Output of frequencies in maps only if the frequencies are within the range defined by the user (exception: center-of-mass frequency map).
• Output of a frequency histogram (the bin size is defined by the user in the settings dialog):
  
• Primary and secondary frequency peak in the APS are now also plotted in the APS plot:
  
• Settings dialog with more explanations:
  

Version v0.2.3 - Bug fixes & improved output

Bug fixes:

• A filter was removed that blocked the output of frequencies that were higher than a quarter of the acquisition frequency in the main output text file. In previous versions, such frequencies were replaced by NaN and output as a blank in the text files.
• In previous versions, phase maps referring to results from the "signal" area only indicated a value of 0 at non-signal areas. In such plots, from now on, non-signal regions are shown in black (not indicating any number).

News:

• Output of all produced maps (e.g., for frequency or phase) as tab-delimited text files, showing the exact number for each pixel, which provides a better accessibility for post-hoc analysis. Undetermined pixels are shown as blank.
• Output maps in the PNG format (instead of TIF format) to save memory for storage of the output files.

Version v0.2.2 - update dialog to add files

First public release, linked to a digital object identifier (DOI) on zenodo.

Changes compared to previous version:

• From now on the plugin is launched through the menu entry Plugins > JNH > Cilility > Cilility analysis v0.2.2
• Updated the dialog to open files for batch-processing
• Added explanations to the settings dialog
• Cleaned up code
• Added more information to read-me file

Version v0.2.1 - Initial online release

ReduceMemoryAddPhasePlotOfConstantFreq

- Reduce memory
- Add phase plots for specific frequencies
- Remove Eigenvectormaps as not indicative
- Add try-catch clause to prohibit interruption if analysis of one file crashes