MicrobeTracker Tools

This page contains a brief description of the available tools that supplement MicrobeTracker. Click the name of a particular tool to get more information. For the description of the data format, in particular the cellList structure, refer to Output Format section of MicrobeTracker manual.

All these commands run under MATLAB, some will be also compiled into stand-alone versions. When running from MATLAB it is generally suggested to add the folder with MicrobeTracker package to MATLAB path (File>Set Path>Add with Subfolders, then select the folder) and select the folder (or a close upper-level folder) with your data as the working folder in MATLAB, this will allow to select the data fast.

Many of the tools that display results require an array containing cell meshes produced by MicrobeTracker or by SpotFinder family tools. This array could be loaded by dragging and dropping the results file into the MATLAB workspace. Alternatively, MATLAB's load command or MATLAB's variable editor menu can be used to load the array. The name of the array in the file is cellList.

To get help about the functions follow the links on this page or type 'help <function_name>' in MATLAB workspace (providing the name of the appropriate function, e.g. 'help renfiles').

List of tools:

Preparation of images and files

  • renfiles - renames and sorts TIFF (.tif) files produced by common software for MicrobeTracker use.

  • renfilestc - renames and sorts TIFF (.tif) files produced in time courses by Nikon Elements software for MicrobeTracker use.

  • integdic - a tool for conversion of differential interference contrast (DIC) images into a format suitable for MicrobeTracker.

  • aligntool - a tool for semi-manual image alignment of timelapse series with large drift between frames.

Tracking cells

  • trackstack - an alternative tool for tracking cells detected but not tracked previously with MicrobeTracker. Primarily intended for actively moving cells.

Cell dimensions statistics

  • cellstat - basic statistics on an experiment

  • lengthhist - histogram of the length of all cells in a population.

  • meanwidthhist - histogram of the mean width of all cells in a population.

  • maxwidthhist - histogram of the max width of all cells in a population.

Cell intensity statistics

  • inthist - histogram of the total intensity for every cell in a population.

  • meaninthist - histogram of the mean intensity (i.e. divided by the area) for every cell in a population.

  • intprofile - intensity profile for a single cell.

  • intprofileall - intensity profiles for a every cell in a file saved into a folder.

  • kymograph - kymograph of fluorescence signal in a cell.

  • intdynamics - intensity dynamics of fluorescence signal in a single cell in a time-lapse series.

  • meanintdynamics - intensity dynamics of fluorescence signal in a time-lapse / time-course series averaged for all cells in a given timepoint.

Spot detection

  • spotFinderZ - detects round, usually diffraction-limited spots inside bacterial cells outlined with MicrobeTracker and places them into cellList structure.

  • spotFinderM - manual version of SpotFinder, allows the user to click on spots and records them into the same cellList structure.

  • peakfinder - an alternative to SpotFinder, using a signal profile to detect the peaks, which are saved as spots.

  • spotFinderF - a simplified version of SpotFinderZ, which works in the absence of cell data, i.e. finds spots on images.

  • joinspots - a tool for semi-automatic linking spots detected with SpotFinder family tools between frames.

Spot statistics

  • spotnumhist - histogram of the number of spots per cell in a population.

  • spotvslength - diagram of the number of spots per cell vs. cell length.

  • spotinthist - histogram of the intensity of all detected spots in all cells in a population.

  • spotposhist - histogram of the position of spots inside cells.

Displaying cells and spots

  • dispcell - displays one cell with the spots inside on top of the image.

  • dispcellall - displays all cells in a given range of frames with the number of spots and the intensity of the spots and their relative position in given range.

  • dispcellrid - same as dispcellall above, but displays the cells cropped and placed in a grid.

  • cellmovie - displays or saves a movie or a time series of images of a single cell (with or without spots).

Cell curvature

  • getcurvature - obtains the radius of curvature of every cell in a list.

  • curvhist - histogram of the curvature (or radius of curvature) of the cells.

Exporting and importing data

  • loadimageseries - loads a series of TIFF images into a 3D array.

  • loadimagestack - loads an image stack file into a 3D array.

  • saveimageseries - saves a 3D array of images into a series of TIFF files.

  • saveimagestack - saves a 3D array of images into a multipage TIFF file.

  • exportcells2xls - saves the cell dimensions and signal data produced by MicrobeTracker into an Excel or CSV file.

  • exportspots2xls - saves the spots data produced by the SpotFinder family tools into an Excel or CSV file.