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ProkaryMetrics is a software package designed to provide:

  • 3D reconstruction and visualization of 8/16-bit B&W fluorescent microscopy z-stacks
  • 3D interaction with the reconstructed data
  • manually-assisted annotation of the individuals in microbial biofilms
  • visual and quantitative analysis tools to gather quantitative measurements on individuals as well as the biofilm as a whole

Software Requirements

The software is written in Python (2.7) and requires the following libraries:

  • VTK (the Visualization Toolkit). At least version 5.6.
  • wxPython (windowing toolkit). At least version 2.8.10.
  • PIL (the Python Imaging Library). At least version 1.1.7.

The simplest means to getting the appropriate Python environment with the appropriate libraries is to install the Enthought Python Distribution (free for Academic users) which can be found at:

ProkaryMetrics requires at least version 7.0 to run due to the need for Python 2.7.

In the near future, I hope to provide a self-contained app package for Mac/Win that will not require any installations.

Running ProkaryMetrics

Once you have the appropriate Python environment and libraries installed, use a console to navigate to the ProkaryMetrics folder contained with this file in the downloaded archive and type:

$> python

This command will launch the program, and everything else is done through interacting with the GUI.

User Interface

Below is a screenshot of the basic user interface for ProkaryMetrics. The major interface elements are highlighted, as well as the important data kept track of at all times.

  1. Visualization Window - This is the main focus of ProkaryMetrics; providing the user with 3D visualization of their reconstructed data, and allowing mouse-interaction for 3D data manipulation and exploration.
  2. Actions Panel - This section of the program window provides the count of bacteria the user has marked, and presents the option to either save a set of marked points as a bacterium, or undo the addition of the last recorded bacterium.
  3. Status Bar - The status bar is divided into four sections. From left to right: the most recent status message (seen here, the successful loading of a saved project), the current mouse pointer location in terms of X, Y, and Z within the rendered data, the mouse click mode (Exploring allows the user to examine the data by rotating, zooming, etc..., the other option Recording allows the user to annotate bacteria), and the camera mode (this feature is still in testing).
  4. Mouse Cursor - The red and green cones represent the location of the mouse, with the clicking tip between the points of the cones. The two-cones cursor attaches itself to the nearest surface of the reconstructed data, allowing the user to trace the surface and thus permit accurate marking of bacteria. Here the cursor is tracing the surface of a section of the image data (green) representing a bacterium. The orange data is a user-recorded marking of the bacterium from the image data.

Updating ProkaryMetrics

The latest version of the software is always available through the main website: