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Data Interaction

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ProkaryMetrics is designed to reconstruct volumetric image data by combining sets of 2D images known as z-stacks that represent optical slices of a physical data sample. Currently the default image format used by ProkaryMetrics is the Tagged Image File Format (TIFF), but the software also supports JPEG images.

Opening Files

Image data is added to the current rendering window through the File >> Open Image File(s)... menu item. Since a z-stack is expected, the file selection dialog will accept multiple file selection.


Clicking the “Open” button will cause ProkaryMetrics to attempt to load the specified image files, and render a 3D surface representation of the fluorescent pixels (see the User Interface subsection in the Introduction section). Currently, ProkaryMetrics has a default pixel-brightness level it uses when performing the 3D reconstruction, which will not be appropriate for all image data. Particularly, 8-bit image data which only has pixel values between 0 and 127 will not be properly reconstructed initially. If the reconstructed data does not look right, or does not appear at all, you can modify the pixel value used to perform the reconstruction. This and other user-modifiable settings are described in detail in the Data Interaction section. Eventually the initial value will be intelligently chosen using the content of the image data itself, but users may still want to tweak the setting.


Once you have loaded some image data and maybe marked some bacteria, you will want to save your work. ProkaryMetrics supports saving and loading of project files. A project consists of the current state of the program including all loaded image files, any recorded bacteria, and any modified settings. Both saving and loading projects can be done through the File menu.

Note that ProkaryMetrics does not store a copy of the loaded image data, it merely stores the location of each loaded image file. This means when you load a previously saved project file ProkaryMetrics will look for the image data in the location it was when you saved the project. If the images have been moved or deleted it will pop up a message telling you it cannot locate them, and will give you the option to select the folder they have been moved to. If it can find all the images in the new location, it will load them and continue loading the rest of the project information.


Given that one of the main goals of ProkaryMetrics is to provide quantitative and statistical information about microbial communities, it is often useful to use that data in other software for additional analysis or display. To this end, ProkaryMetrics provides the facility to export certain data. Currently, this includes: bacteria and lengths. Both options are available through the File >> Export menu.


Exporting bacteria will result in a file that lists the marked end and interior points for each bacterium. Each line corresponds to an individual bacterium, and each line is a comma-separated list of 3-tuples that indicate the X, Y, and Z coordinates of each marker that makes up the recorded bacterium.

1.23, 3.44, 0.65, 18.36, 4.40, 2.21

This example shows a line of 6 numbers separated by commas. As mentioned above, the line is logically grouped into 3-tuples indicating axis values. This line has 6 values, and so indicates two markers representing a single bacterium.


The export lengths option creates a single-column CSV file with a header line of “len”. Each line in the file gives the length of a single bacterium in micrometers.