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
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
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
Cell dimensions statistics
cellstat - basic
statistics on an experiment
lengthhist - histogram
of the length of all cells in a population.
histogram of the mean width of all cells in a population.
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
intprofile - intensity
profile for a single cell.
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.
intensity dynamics of fluorescence signal in a time-lapse / time-course series
averaged for all cells in a given timepoint.
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
spotnumhist - histogram
of the number of spots per cell in a
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.
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
cellmovie - displays or saves
a movie or a time series of images of a single cell (with or without spots).
Exporting and importing data
loads a series of TIFF images into a 3D array.
loads an image stack file into a 3D array.
saves a 3D array of images into a series of TIFF files.
saves a 3D array of images into a multipage TIFF file.
saves the cell dimensions and signal data produced by MicrobeTracker into an Excel or CSV file.
saves the spots data produced by the SpotFinder family tools into an Excel or CSV file.