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Puncta Process

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The Puncta Process ImageJ PlugIn is a practical analysis tool for counting puncta in 3D image data.

The plugin uses single-channel data to produce three specific values:

  • Puncta Volume An average number of voxels (volume picture elements) of the object times z,y, and z calibrations.
  • Puncta Number The average number of puncta counts within a given ROI (Region of Interest)
  • ROI Intensity The measures the overall pixel intensity over the Region of Interest

The Puncta Process expects that the preprocessing step of selecting the ROIs has been completed and that the image data is separated into a directory structure based on fluorescence (488, 561)

The Puncta Process leverages the MorphoLibJ and 3D Objects Counter PlugIns and allows users to select Filter options and threshold levels prior to process execution.

The process provides detailed outputs of each process step, including:

  • White Top Hat corrected images
  • 3D Object Counter details (CSV)
  • Z Projected images (maximum intensity)

And a summary output including:

  • MS Excel Report
  • Preliminary Visualizations BarCharts with Error bar
  • Summary CSV data (for ease of import into downstream processes)


  • In Fiji), you just need to add the Puncta Process and IJPB-plugins sites to your list of update sites:
    1. Select HelpUpdate… from the menu to start the updater.
    2. Click on Manage update sites. This brings up a dialog where you can activate additional update sites.
    3. Activate the Puncta Process and IJPB-plugins sites and close the dialog.
    4. Click Apply changes and restart ImageJ.


The main source code directory is on GitHub under here.