Output Format

MicrobeTracker saves data in MATLAB format, creating standard .mat files, which can be opened with MATLAB without running MicrobeTracker. Among other variables, it saves the variable cellList, the only one that is intended for the user. To load a saved file in MATLAB, just drag and drop it into the open window or use the load command.

The hierarchical organization of the variable is shown in the image above. It is a MATLAB cell array, with each cell of the arragy corresponding to one image frame. Each cell of this cell (subarray) is in turn a cell array corresponding to a real (that is, biological!) cell. Each of those is a structure with several fields describing different properties of the cell. For example, to access the field "algorithm" for the cell 4 on frame 5 type: "cellList{5}{4}.algorithm". The fields of this structure are:

  • algorithm - the algorithm used to obtain meshes, see Parameters section.
  • birthframe - the frame on which the cell first appeared in a timelapse. It is equal to the frame number for independent frames.
  • model - the data set describing the shape in MicrobeTracker units, it is only used by MicrobeTracker to continue detection in timelapses.
  • mesh - the data set describing the shape in geometrical units. This is a Nx4 matrix (N rows and 4 columns) with the structure shown on the image to the right. The left two rows of the matrix correspond to the left side of the cell, for the x and y coordinates respectively. The right two columns correspond to the right side of the cell. The first row corresponds to the first pair of points (a cell pole), the second - to the second pair of points etc. If the cell is aligned (i.e. its polarity is set either manually or automatically during divisions), then the first row corresponds to the "old pole", otherwise the vertical orientation of the matrix is random.
  • polarity - this property indicates whether the polarity is set (polarity=1) or not set (polarity=0).
  • ancestors/descendents - the list of ancestors or descendents in genealogical order. If a cell divides, one of the two ("mother") keeps the number, and the other ("daughter") gets a new one. The daughter keeps the number of the mother, as well as the grandmother, great-grandmother etc. in the field ancestors. The mother in turn remember the names of each daughter in the field descendents. For a more detailed description of cell numbering see Cell Numbering page.
  • divisions - the frame numbers of each division this cell came through as the mother. The daughter remembers only the frame when it split of as birthframe.
  • timelapse - indicates whether the cell is a part of a time-lapse series.
  • box - the box coordinates (1x4 array with the format: top x, top y, width, height), that includes the mesh inside. It should be used if cropping the fragment of the image that contains this particular cell.
  • length/area/volume - the length, area, and volume of the cell. The length is the length of the centerline. The area is the area inside the mesh outline. The volume is estimated by assuming the height of each segment is the same as its width and calculated by summing the volume of the cut cones corresponding to each segment.
  • steplength/steparea/stepvolume - the length, area, and volume of each segment of the mesh inside the cell. the order is from the old pole to the new one when the polarity is set, or randomly beginning from one side, if not.
  • lengthvector - the coordinates along the centerline of the centers of each segment. The spacing can be different from the default of 1 pixel and the polar segments can be different from the set spacing, thus this variable is more accurate than the number of the row to represent the coordinate.
  • signal0/signal1/signal2 - the calculated signal along the cell. Usually signal0 is reserved for the phase contrast, signal1 for the images loaded as signal 1 etc.; those these names can be changed (see Detection and analysis section).
  • spots - unlike the rest of the he fields, this one is added by spot dection tools, sych as a SpotFinderM, SpotFinderZ, or peakfinder. This field is a separate structure that contains information about the location and intensity of spots detected in a cell. For a detailed description, see the SpotFinder help page.