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August 20, 2019. New version 1.3.4 of PointDensitySyn.

  • Added input file information to interpoint distance output.
  • Minor bug fixes to ImageJ plugin and Python component.

August 7, 2019. New version 1.2.4 of PointDensity.

  • Added input file information to interpoint distance output.
  • Minor bug fix.

June 15, 2018. New version 1.1.0 of PlotProfile.

  • Added batch plotting, allowing automatic saving of plots of all coordinate files in a folder.
  • Other minor changes and bug fixes.

June 13, 2018. New version 1.0.0 of PlotProfile.

  • Added a "Plot next" button, that selects and plots the next file in the current folder, making it easier to cycle through all files in a folder.
  • Other minor changes and bug fixes.

June 13, 2018. New version 1.3.3 of PointDensitySyn.

  • Fixed bug that caused an incorrectly adjusted PSD if the PSD outline crossed the specific segment of plasma membrane between the last and first end nodes of the membrane.

June 11, 2018. New version 1.1.3 of Vesicle.

  • Fixed bug in the ImageJ plugin that caused a conflict with the Synapse plugin if that plugin was also present in the plugins folder.

June 1, 2018. New version 1.0.0 of ParticleDensityDouble.

  • Migrated to Python 3.
  • Now saves .xlsx Excel files instead of old .xls files.
  • Particles outside Monte Carlo simulation window can now be excluded when calculating interpoint distances, which allows for better comparison with simulated points.
  • Processed coordinates, including simulated points and convex hulls of particle clusters, can now be saved for plotting using PlotProfile.py.
  • Increased the number of decimals (i.e., accuracy) used for pixel width in coordinate files saved by the ImageJ plugin to 4.
  • Other minor changes.

May 31, 2018. New version 1.1.2 of Vesicle.

  • Fixed interpoint and intervesicle distances.
  • Other minor changes.

May 31, 2018. New versions of DistToPath, PointDensity, PointDensitySyn and Synapse.

  • Fixed bug introduced after migration to Python 3 that could cause truncation of columns in interpoint distance summaries when using random points.

May 28, 2018. New version 1.1.1 of Vesicle.

  • Fixed bug introduced in version 1.1.0 that caused the particle area density in the profile summary to not exclude holes from the total area.

May 25, 2018. New version 1.2.2 of PointDensity and new version 1.3.1 of PointDensitySyn.

  • Fixed bug introduced in versions 1.2.0 and 1.1.0 of PointDensity and PointDensitySyn, respectively, that caused the calculation of particle area density in the profile summary to not exclude holes from the total area.

May 25, 2018. Version 1.1.0 of Vesicle released.

  • Now works with Python 3.
  • Now saves .xlsx .Excel files rather than the old .xls format.
  • Other minor changes.

May 24, 2018. New version 1.3.0 of PointDensitySyn.

  • Particles outside Monte Carlo simulation window can now be excluded when calculating interpoint distances, which allows for better comparison with simulated points.
  • Processed coordinates, including simulated points and convex hulls of particle clusters, can now be saved for plotting using PlotProfile.py.
  • Removed option to choose which summary files to save.
  • Fixed bug that prevented csv files from being written.
  • Fixed a bug in the packaging of Windows binaries that caused failure to write Excel files.
  • Other minor bugs and changes.

May 24, 2018. Version 1.2.1 of PointDensity released.

  • Fixed critical bug that caused the Python component to fail to process files when no previous log file existed.
  • Fixed bug that prevented csv files from being written.
  • Fixed a bug in the packaging of Windows binaries that caused failure to write Excel files.

May 24, 2018. Version 1.0.0 of Vesicle released.

  • Fixed a bug that prevented the ImageJ plugin from showing up in the menu.
  • Added calculation of vesicle Feret diameter.
  • Minor changes.

May 22, 2018. Version 0.2.0 of PlotProfile released.

  • Convex hulls of particle clusters can now be plotted.
  • Adjusted marker sizes of particles and simulated points.
  • Fixed bug that caused failure to save options.

May 18, 2018. Initial release (version 0.1.0) of PlotProfile.

  • This tool allows simple plotting (using the Matplotlib library) of profiles from coordinate files generated by any of the immunogold analysis tools. These plots can be saved in either vector or raster image formats.

May 8, 2018. Version 2.0.2 of DistToPath released.

  • Fixed a critical bug, introduced in version 2.0.0, that triggered an error when encountering particles with a negative distance to path.
  • Fixed a bug that caused 'Negative shell' Monte Carlo simulation window to fail.
  • Now shows a warning when determining interpoint distances between particles and simulated points while using a simulation window other than 'Shell'.
  • Changed icon.

May 8, 2018. Version 1.2.0 of PointDensitySyn released.

  • Fixed bug preventing use of PSD as a Monte Carlo simulation window.
  • PSD simulation window now works also with non-strict location.
  • Changed icon.
  • Other minor changes.

May 4, 2018. Version 1.2.0 of Synapse released.

  • The Python component now saves Excel output in the .xlsx format, and uses Python 3 instead of Python 2.
  • Added a 'Postsynaptic density' Monte Carlo simulation window option.
  • Minor bug fixes and other changes.

April 25, 2018. Version 1.1.0 of PointDensitySyn released.

  • The Python component now saves Excel output in the .xlsx format, and uses Python 3 instead of Python 2.

April 20, 2018. Version 1.2.0 of PointDensity released.

  • The Python component now outputs profile Feret diameter, and saves Excel output in the .xlsx format.
  • The Python component now uses Python 3 instead of Python 2.

April 20, 2018. Version 2.0.1 of DistToPath released.

  • Minor bug fix.

April 17, 2018. Version 2.0.0 of DistToPath released.

  • The Python component now supports Monte Carlo simulations, interpoint distances and clusters. It also saves Excel output in the .xlsx format rather than old Excel 2003 .xls format.
  • The Python component now uses Python 3 instead of Python 2.

October 6, 2016. Version 1.0 of PointDensitySyn released.

  • The Python component now explicitly calculates normalized lateral distance of points to the PSD/active zone, as well as the distance to the synaptic membrane of simulated points that project orthogonally on the synaptic membrane.
  • Bug fixes in both components.

May 16, 2016. New version of PointDensitySyn.

  • Bug fix.

April 21, 2015. New versions of ParticleDensityDouble, PointDensitySyn and Vesicle released.

  • Bug fixes and code cleanup in the Python components.

April 20, 2015. Version 1.1.1 of PointDensity released.

  • Bug fixes and code cleanup in the Python component.

March 9, 2015. A book chapter on quantitative analysis of immunogold labeling published.

  • Vidar Gundersen, Linda H Bergersen and I have just published a book chapter on quantitative analysis of immunogold labeling, including an introduction to these software tools. The chapter is in the book Immunocytochemistry and Related Techniques, Neuromethods, vol 101 (edited by Adalberto Merighi and Laura Lossi).

December 19, 2014. Version 1.0.2 of DistToPath released.

  • Fixed another critical bug introduced in version 1.0.0.

December 19, 2014. Version 1.0.1 of DistToPath released.

  • Fixed a couple of critical bugs, introduced in version 1.0.0, in the Python component.

November 11, 2014. First public version of Vesicle.

November 11, 2014. New versions of DistToPath, ParticleDensityDouble, PointDensity, PointDensitySyn, and Synapse.

  • In all tools, the ImageJ plugin now uses image overlays for profile components. This means that the components can be easily modified or deleted until the profile is saved.
  • In all tools, the Python component and ImageJ plugin were subject to code cleanup and miscellaneous changes and bug fixes.
  • The license for all tools was changed to the MIT license.

August 14, 2014. New version of PointDensitySyn.

  • Minor changes and bug fixes.

May 14, 2014. New versions of DistToPath, ParticleDensityDouble, PointDensity, PointDensitySyn, and Synapse.

  • In ParticleDensityDouble, modified the user interface of the Python component; it should now look fine also on platforms other than Windows. The UI is now also threaded.
  • In ParticleDensityDouble, current options can now be saved in a configuration file in the user's home directory.
  • In PointDensity, fixed a bug in the Python component that caused output files for random and grid points to instead show the corresponding values for the recorded points.
  • In PointDensity, fixed a bug that caused simulated particles within profile holes to be accepted as valid when simulation window was set to "profile + shell".
  • In DistToPath, ParticleDensityDouble, PointDensity, and PointDensitySyn, fixed a bug that caused the Windows binary version of the Python component to not be able to write Excel files.
  • Other minor bug fixes and changes.

May 13, 2014. First public versions of DistToRandomLine and ParticleDensityRandomBox.

May 7, 2014. New versions of Synapse and DistToPath.

  • In Synapse, fixed a critical bug introduced in the previous version of the Python component.
  • In DistToPath, modified the user interface of the Python component. It should now look fine also on platforms other than Windows. Processing is now also cancellable via a progress dialog.  
  • In DistToPath, current options can now be saved to a configuration file in the user's home directory.
  • Various other minor bug fixes and changes.

April 23, 2014. New versions of DistToPath and ParticleDensityDouble.

  • Adjusted some interface elements in the Python components so that they are no longer partly obscured when using newer versions of wxPython. However, note that I only regularly test the tools using ordinary settings in Windows. If you experience problems using other systems, please let me know.

January 27, 2014. New versions of PointDensity, PointDensitySyn and Synapse.

  • Fixed a bug that caused a failure to execute the Python component of these tools when using wxPython 2.9+ (this does not affect the pre-built Windows binaries). Note: in the Python components of DistToPath and ParticleDensityDouble, some text is obscured when using wxPython 2.9+. I will try to fix this as soon as possible. In the meantime, use the Windows binaries or wxPython 2.8.12.1 (which can be downloaded from SourceForge).

November 15, 2013. New version of ParticleDensityDouble.

  • Fixed a bug that prevented random regions of interest (ROIs) generated by Place random ROI to be used to define profile border (or hole).
  • Rectangular ROIs in general may now be used to define profile borders or holes.

November 13, 2013. New version of ParticleDensityDouble.

  • Fixed a bug in the Python component that produced a parsing error for input files not containing random points.
  • Minor bug fixes.

August 13, 2012. New version 1.0pre4 of PointDensity.

  • Fixed some compilation warnings in the ImageJ plugin.

August 8, 2012. New version 1.0pre3 of PointDensitySyn.

  • Fixed a bug in the Python component that caused an error with input files that do not contain random points.
  • Fixed a minor bug and some compilation warnings in the ImageJ plugin.

July 13, 2012. New version 1.0pre3 of PointDensity.

  • Fixed a bug that caused an error when calculating interpoint distances from an input file without random points.

October 17, 2011. New version 1.0pre2 of PointDensitySyn.

  • Fixed a couple of minor bugs.

October 14, 2011. New version 1.0pre2 of PointDensity.

  • Fixed a couple of minor bugs.

December 15, 2010. New version of ParticleDensityDouble.

  • Rewrote and cleaned up some code.
  • A few minor changes and bug fixes.

September 29, 2010. The .zip files containing the most recent versions of PointDensity and PointDensitySyn were apparently corrupt, and were therefore replaced.

September 3, 2010. New versions of PointDensity, PointDensitySyn and Synapse.

  • PointDensity and PointDensitySyn can now calculate interpoint distances between points and simulated points.
  • PointDensity and PointDensitySyn have the option to specify Monte Carlo simulation window.
  • An abortable progress dialog is now shown in PointDensity and PointDensitySyn during processing.
  • Options may now be saved to a configuration file in the user's home directory. Options specified in this file are loaded when the program starts.
  • In Synapse, points outside the shell are now discarded. This also neutralizes a bug where the number of simulated points when using the whole profile (i.e., profile and shell) as simulation window was set to be the same as the total number of particles, including those outside the shell.
  • Fixed a bug in Synapse where a lateral interpoint distance of 0 between a pair of points or between a point and a random point would be written as an empty cell in the output file.
  • A number of minor bug fixes and changes.

August 11, 2010. Added add_random.py and change_scale.py, small scripts used to alter batches of coordinate files generated by the tools.

June 17, 2010. Synapse version 1.0 released.

  • Cleaned up the user interface of the Python component.
  • Processing is now abortable via a progress dialog.
  • Various other small changes and bug fixes.

June 1, 2010. New versions of PointDensity and PointDensitySyn.

  • Cleaned up the user interface of the Python components of PointDensity and PointDensitySyn. They should now show properly also on non-Windows platforms.
  • Various small changes and bug fixes.

 


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Last updated: 2019-08-20