Text-based Batch Mode

MicrobeTracker has two variants of the batch-processing mode: graphical and text-based. The text-based batch mode is called from the graphical one by clicking the Text mode button. The graphical mode window will then be replaced with the text-based one. The window is a simple text editor, which allows the user to type, save and load text files. The same files can also be prepared in any external text editor. This window is designed to prepare a simple script, which is interpreted by MicrobeTracker when the user clicks Run. MirobeTracker can run both standard MATLAB functions and the internal MicrobeTracker functions, not accessible otherwise. This mode provides in principle wider possibilities than the graphical mode because any MicrobeRacker function can be run inside it. However, the text-based mode is more error-prone and has only been tested with a limited number of funtions. Therefore, it should be used with caution.

List of basic MicrobeTracker functions

Example

Here is an example of a script, which can be run in text-based batch mode:

  loadimages(1,'C:\images')
  loadparams('C:\meshes2.mat');
  process([],1,[],0,'','',0,0,[])
  savemesh('C:\meshes2.mat',[],0,[])

The first line of script loads the images from folder C:\images\ (here Windows fomat is assumed, replace back slashes to forward slashes for Linux/Mac). The second line loads the parameters from an analysis file meshes2.mat on drive C:. The third line does cell detection on all loaded frames in Timelapse mode. The fourth line saves the analysis to file meshes2.mat.

 

Top pages: Buttons and Controls, MicrobeTracker Suite.