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

  • loadimages(channel,folder) - loads a series of TIFF images from a folder. It takes 2 parameters: folder - the name of the folder with the images; and channel - the channel to which the images will be loaded, this is a number 1,3, or 4: 1 for "phase", 3 for "signal 1", and 4 for "signal 2". Note that folder and file names either start in the current MATLAB folder, or are full paths starting with a drive letter.
  • loadstackimages(channel,file) - loads a set of images from a stack file using Bioformats (must be available). It takes two parameters: file - the source file name, and channel - same as above.
  • loadaram(file) - loads a set of saved parameters from a file file. The parameters are assigned to an internal variable which remains the same until it is changed by such command as loadparam, parseparams (see below), edit2p (to grab the parameters from MicrobeTracker's Parameters control). Therefore, parameters must be initialized at the beginning, but no reassignment of parameters is necessary to process a new set of images.
  • param = loadmesh(filename) - loads analysis (meshes) from file filename. Optional output is the parameters string, in case you need to load it as well (it does not assign these parameters to the internal varaible and therefore they would not be used in cell detection. End this commant with a semicolon, unless you want the parameters to bi displayed in MATLAB's command window.
  • parseparams(param) - initializes the internal parameter variable with the string param obtained by loadmesh command. Run this command to actually use the parameters in cell detection.
  • alignfrm - aligns the frames (loaded at the moment).
  • savealign(filename) - saves the alignment data to file filename.
  • loadalign(filename) - loads the alignment data from file filename.
  • subtractbgr(channels,range,invert) - subtract background from channels (a number 3 or 4, or array [3 4], 3 for signal 1, 4 for signal 2). range - range of frames to process, a two-number array, an empty array or a single number. invert - 0 or 1, 0 for phase-contrast (dark on light background) images used to detect cells, 1 for fluoresnce images (light on dark background) used to detect cells.
  • process(range,mode,lst,addsig,addas,savefile,fsave,saveselect,region) - the main processing command, which depends on 9 parameters:
    • range - range of frames (an array of two numbers or a single number) on which the processing will be made or an empty array for all frames, e.g. [1 10] for frames from 1 to 10, [] for all frames.
    • mode - 1-Timelapse, 2-1st independent frame, 3-Independent frames, 4-Reuse meshes.
    • lst - list of cells to be processed, defined on the frame preceeding the first frame in the range (if detection is performed) or on any frame (in Reuse meshes mode). Use the empty array [] to process all cells.
    • addsig - an array of four numbers 0 or 1, indicating whether to add signal to each channel (as above: 1-phase, 3-signal 1, 4-signal 2).
    • addas - a cell array of values indicating the names under which the signals will be saved. Default {}, which is equivalent to {0,-,1,2}. Each numeric value X is converted to signalX, each string value remains unchanged. I.e. {0,0,'s1',200} will save the profile of the phase signal to field "signal0", signal 1 to field "s1", signal 2 to field "signal200".
    • savefile - filename to save the analysis while processing (such as 'tempresults.mat' in the main window). Provide an enpty string '' if no saving is necessary.
    • fsave - "frequency" of saveing, i.e. the number of frames per one saving.
    • saveselect - 1 to save only selected cells and 0 to save all cells.
    • region - region to process (an array of four numbers, left-top- width-height), [] for the whole image.
  • savemesh(filename,list,mode,range) - save the analysis, list - list of selected cells (or an empty array), mode - 1 (true) to save only the selected cells, 0 (false) - to save all cells, range - range of frames (as above, a two-element array, an empty array or a number).


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


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.