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##Release Notes for Sholl Analysis

The latest release build is available through the Fiji Updater or from the plugin's webpage. Development builds may have new features (see Wish List) but are bug-prone and probably undocumented. They are pushed to the Fiji Updater once new features mature and no major issues are found. Pre-compiled binaries (and respective sources) of the versions listed here can be downloaded from jenkins.imagej.net or from the releases page.

Development Builds

  • UI Improvements:
    • Exit messages with tooltips (#8)
    • Table tweaks: Auto-formatting of decimal places; Plot tables without row numbers; Distance unit is reported on a dedicated column (#9)
  • Minimum requirements: ImageJ 1.49i.

Release Builds

####Version 3.4.3 (October 2014) DOI

  • Analysis of tabular data:
    • Improvement: Analysis can be restricted to selected rows
    • Fixed: Parameters such as Radius Step, Starting radius, etc., were being calculated every time a choice was made in the dialog prompt. This was spurious, and could cause the plugin to abort
    • Fixed: Exception triggered when Intersections column contained no numeric data
    • Fixed: Reported Radius Step was innacurate: it was being extracted from the difference between the first two rows in Intersections column rather than Distance column. This was due to a silly overlook
  • Bitmap analysis:
    • Fixed: Cf. Segmentation could not parse binary images with display ranges other than 0-255
  • General:
    • Fixed: Auto-restart triggered by the Analyze Sample Image command was unreliable
    • Improvement: Enclosing radius is now set to NaN if the respective cutoff is not met
    • Improvement: Ensure coherence in abbreviations (some metrics were reported using multiple abbreviations)

####Version 3.4.2 (July 2014) DOI

  • Fitting to higher order polynomials is now possible using a BAR command (documentation: GitHub, Fiji)
  • Added Mode to the list of choices for integration of multiple samples (2D images)
  • Improved user interface:
    • Macro/script recording: The Alt key modifier is now logged, so that users no longer need to find out how to trigger the key event in their macros
    • Tooltips are displayed in the ImageJ status bar when key options are specified
    • Dialog for tabular (CSV) data is much interactive and imported data can be replaced at any time using the Import Other Data command
    • With error messages, the plugin now auto-restarts when user chooses to analyze the ddaC sample image (File>Open Samples>ddaC Neuron) or when the imported CSV data is not valid
    • Users can shuttle between Bitmap and CSV modes by dismissing prompts while holding the Alt key
  • Bug fixes:
    • Fixed a bug that made the Macro Recorder to record an invalid command after pressing Cf. Segmentation
    • Fixed a but that did not give users the opportunity to save the Results table before it would be cleared by the plugin
    • Fixed a but that caused some settings to be logged as NaN when analysing CSV data

####Version 3.4.1 (March 2014)

  • Improved prompts: live validation for Ending radius/Radius step size. Center of analysis is displayed on status bar. Section headings are clickable URLs pointing to respective section of the manual
  • Added Cf. Segmentation, that allow users to confirm which phase of the image is being sampled. This should help inexperienced users to make sure they are measuring neuronal processes and not the interstitial spaces between them.

####Version 3.4.0 (January 2014)

  • Guesses which of the normalization methods (semi-log or log-log) is the most informative using the concept of determination ratio
  • Added 2nd and 3rd polynomials as fitting choices
  • Dialog becomes scrollable if larger than 80% of screen height/width. This ensures dialog prompts are displayed properly on small laptops such as netbooks
  • If the same image is repeatedly analyzed, detailed data from previous analysis is discarded
  • Fixed: macros calling the plugin could not parse filenames containing spaces
  • Versioning conforms with SemVer

Unfortunately, the numbering scheme used up to version 3.4.0 is somewhat arbitrary and not that meaningful. However, large increments usually indicate changes in the user interface.

####Version 3.3 (December 2013)

  • 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 (June 2013)

  • Hold dow Alt to analyze profiles obtained elsewhere, including those from 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 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
  • 3D Sholl: Option to ignore isolated (noise) voxels
  • 3D Sholl: Minimized rounding errors related to digitization of spheres
  • 2D Sholl: Replaced 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
  • 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 v2.0
  • Checks for reasonable Radius span values

####Version 2.0

  • Curve Fitting, modernization of Tom's code

####Version 1.0

  • Initial version by Tom Maddock

Wish List

  • Fitting to polynomials of higher degree (Version 3.4.2)
  • Restrict analysis to area ROIs (rather than hemicircles/spheres?)
  • Obtain a mask for every chosen method (slices of an ImageStack?)