ASA/Notes at master · HansLui/ASA · GitHub

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Sholl Analysis, http://fiji.sc/Sholl_Analysis/

WISH LIST
=========
    - Obtain a mask for every chosen method (slices of an ImageStack?)
    - Fix dialog prompt: Can become higher than 700px and may not be displayed on netbooks
    - Restrict analysis to area ROIs (rather than hemicircles/spheres?)


RELEASE NOTES
=============
   (Unfortunately, the numbering scheme is somewhat arbitrary and not that meaningful.
    However, large increments usually indicate changes in the user interface).

Version 3.3 (December 2013) [latest]
    - Calculates skewness and kurtosis for both sampled and fitted data
    - Fixed v3.1 bug in which values from log-log plot were not listed in table

Version 3.2 (August 2013)
    - Enclosing radius is defined as the widest distance associated with a specified
      cutoff value of intersection counts. At the default cutoff (1), it is the largest
      of intersecting radii.

Version 3.1
    - Hold dow "Alt" to analyze profiles obtained elsewhere, including those from Simple
      Neurite Tracer, http://fiji.sc/Simple_Neurite_Tracer
    - Multiple profiles can be obtained at once
    - Plugin can now predict (or at least try) the polynomial of best approximation
    - New descriptors: Median and Barycenter of sampled profile
    - Added a "batch mode" option that saves profiles without displaying them
    - Sholl decay is calculated using the full rage of data or values within percentiles
      10 and 90, which usually provides a better fit. However, Sholl decay is only
      calculated when logarithmic methods are chosen (v2.2 behavior)
    - Normalization can be performed against: Area of circle/Volume of sphere, Perimeter
      of circumference/Surface of sphere or Area of annulus/Volume of spheric shell.
    - Made main dialog more intuitive. This may brake previous macros created with the
      Macro Recorder
    - Barycenter and other descriptors are highlighted on plot
    - Updated the URL of help page to http://fiji.sc/Sholl_Analysis/
    - Eliminated the "Sholl LUT" command (with IJ 1.48a an later LUTs of non-8-bit TIFFs
      are saved with the image)
    - Sholl mask reports only values from "Linear Sholl". "Semi-log" and "Linear-norm."
      masks are no longer created. This could be reinstated if needed

Version 3.0
    - 3D Sholl:
      - Better handling of anisotropic voxels
      - Option to ignore isolated (noise) voxels
      - Minimized rounding errors related to digitization of spheres
    - 2D Sholl:
      - Substituted "Radius span" with "Samples per radius" to avoid misinterpretations of
        the former parameter. A draconian maximum of 10 "Samples per radius" is
        deliberately imposed to encourage "Continuos Sholl"
    - General improvements:
      - 3D and 2D algorithms are ~25% faster (3D analysis remains rather slow)
      - Allows thresholded grayscale images as input
      - Analyzes polarized arbors by restricting the analysis to hemicircles/hemispheres.
        This requires the user to define the center of analysis with an orthogonal radius,
        using the Straight Line Tool and holding Shift
      - Arbor size is calculated as the area/volume of the smallest bounding circle/sphere
        containing the segmented arbor
      - When "End radius" is empty (or NaN), the largest (hemi)circle/sphere is used. This
        allows macros to easily process images without line selections
      - Precision (Scientific notation and number of decimal places) in Sholl table is set
        by "Analyze>Set Measurements..."
      - Sholl mask is coded with Matlab's "jet" color map
      - Major code clean up, which solved several issues
      - Plugin is now registered in the Analyze Menu: "Analyze>Sholl Analysis...".
        Implemented the auxiliary commands "File>Open Samples>ddaC neuron" (2D sample
        image), "Image>Lookup Tables>Sholl LUT" and "Help>About Plugins...>Sholl Plugins"
      - Prettified plot

Version 3d
    - 3D Analysis is now restricted to the volume of each Sholl shell, rather than parsing
      all the segmented voxels

Version 3c
    - 3D Sholl is usable for the first time, but remains extremely slow

Version 3a-b
    - Experimental: Performs 3D Sholl without spike suppression if input image is a stack

Version 2.5
    - Fixed duplicated points in Bresenham's algorithm
    - Option to save data on image directory, if available
    - Long analyses can be aborted by holding Esc

Version 2.4
    - Fixed a 2.3 regression in which -1 tagged pixels were being counted
    - Improved Sholl mask: Minimized rounding errors. Center of analysis is now marked
    - Improved Sholl Table and Plot display

Version 2.3
    - Results are printed to a dedicated table
    - Sholl decay is always calculated
    - Fixed exception in the calculation of critical value in non bell-shaped profiles
    - Impose valid parameters in dialog, rather than keep prompting the user (which was
      not amenable to macro recording)
    - Major code cleaning

Version 2.1-2
    - Fixed several bugs and regressions introduced in version 2.0
    - Checks for reasonable Radius span values

Version 2.0
     - Curve Fitting, modernization of Tom's code

Version 1.0
     - Initial version by Tom Maddock