Syntax:

kymograph(cellList,cell);

kymograph(cellList,cell,[nbins],[frame2time],[pix2mu]);

kymograph(cellList,cell,...,framerange);

kymograph(cellList,cell,...,signal);

kymograph(cellList,cell,...,'area');

kymograph(cellList,cell,...,'volume');

kymograph(cellList,cell,...,'normalize');

kymograph(cellList,cell,...,'nodisp');

kymograph(cellList,cell,...,'integrate');

kymograph(cellList,cell,...,'absolute');

kgraph = kymograph(cellList,cell,...);

This function produces a kymograph of the integrated signal profiles for a single cell in a list of obtained by MicrobeTracker.

• <cellList> - input cell list (the other possible input, which can be used instead of the curvlist). If neither curvlist nor cellList is supplied, the program will request to open a file with the cellList.

• <cell> - the cell to produce a kymorgaph for.

• <nbins> (each argument in square brackets is optional, replace with an empty array [] if not used) - number of bins in the kymograph (the profile is resampled nto a fixed number of bins and is therefore produced in the relative coordinates along the cell to compensate for cell growth; default: 50).

• <frame2time> - conversion factor from frames to time. If not supplied, the kymograph is lotted vs. frame. Note, the first scalar number is interpreted as "nbins" and the second one as "frame2time". In order to only pass "frame2time", use an empty array ([]) for "nbins".

• <pix2mu> - conversion factor from pixels to microns. Only works when 'absolute' parameter is provided. To supply pix2mu but not nbins or frame2time, supply empty arrays ([]) for nbins and frame2time.

<framerange> - two-element array (i.e. for frames from 10 to 20, this array would be [10 20]), indicating the starting and the final frames of a range to use for the kymograph. If not supplied, the program starts from the beginning and proceeds until the cell divides or the end of the list is reached.

• <signal> - the signal field which will be processed. Must be in single quotes and must start with the word 'signal'. Default: 'signal1'.

• 'area' - normalize the profile by the area of each segment producing the average image intensity in each segment.

• 'volume' - normalize the profile by the estimated volume of each segment producing the estimate of signal concentration in each segment.

• 'normalize' - normalize each profile by its sum to compensate for photobleaching of the signal (if known to be constant).

• 'nodisp' - suppress displaying the results as a figure. Note, the function does not produce a new figure by itself. Therefore, you should use the figure command to avoid replotting an existing figure.

• 'integrate' - obtain the values in the kymograpg by integration instead of interpolation of the raw data values. This method is more precise when the number of bins (nbins) exceeds the number of original segments, but is noticeably slower.

• 'absolute' - plot the kymograph in absolute spatial coordinated (pixels or microns, if provided).

• <kgraph> - the output kymograph matrix with the first dimension being the relative position in the cell and the second one being the frame number in the range.