This function plots a histogram of the curvature of all the cells analyzed by Oufti.

This function plots a histogram of the length of all the cells in a population.

This function plots a histogram of the mean width of every cell in a population

This function plots a histogram of the total intensity inside every cell in a population. Note, the background has to be subtracted before detecting the signal in Oufti. The GUI provides users the ability to subtract background from every signal image. This is done by first loading the phase images, followed by signal images.

This function plots a histogram of the mean intensity inside every cell in a population, i.e. total intensity divided by the area of the cell. Note, the background has to be subtracted before detecting the signal in Oufti. The GUI provides users the ability to subtract background from every signal image. This is done by first loading the phase images, followed by signal images.

This function plots the intensity profile for a single cell. Note, the background has to be subtracted before detecting the signal in Oufti. The GUI provides users the ability to subtract background from every signal image. This is done by first loading the phase images, followed by signal images.

The kymograph function produces an intensity heatmap for any signal value in a time-series fashion. In Oufti, the signal profile can be obtained as shown here. Once the signal profile for the different fluorescent signals inside the cells are obtained, the kymograph module can be used to visualize the intensity map of the fluorescent profile over time. The intensity map is created by first computing the interpolation of the original data in fifty equidistant points spanning the interval 0 to 1. This linear interpolation is followed by integration in the interval 0 to 1. This operation is performed on each specified time point and the final result is presented as a kymograph.

This function generates a demograph of the signal profile for a single cell through a time series obtained by Oufti. Demographs are constructed by first integrating the signal values in each segment of the cell mesh and then normalizing the fluorescence in each cell by the maximum integrated value of a particular segment. After this, cells are sorted by the cell length value and the fluorescence values are plotted as a heat map, where 0 corresponds to 0 and 1 to maximum fluorescence signal in the segment of the cell mesh.

This function displays a selected cell, including the contour and all identified spots.

This function displays a full frame including all the detected cells and identified spots (if present).

With this function, users can view the growth curves of individual cells over their entire cell cycle. The function assumes that the cell detection part of the analysis is done prior to using this tool. Assuming the cell detection part is done, users can get a plot similar to the one shown by selecting the Tools tab in the GUI and then pressing on the selection growth curves.

This module allows the user to view subsets of a given population, by filtering cells using parameters shown in the cellListFilter parameters window.



For example, one could desire to see all cells with a length at birth greater than 50 pixels. To filter based on length at birth from the selection window, insert '50' in the box and select the button > as shown below.



Once one of the markers for a given parameter is selected, a plot will be created. This plot will show red lines to represent data points selected through the filtering process, and grey lines to represent all omitted points. This filtered data, as well as original un-filtered data can be saved using the buttons provided in the cellListFilter parameters window.


The fields in the structure returned by the save filtered data button are:

id: Vector of ID numbers of the cells tracked over time.

Lbirth: Vector of length at birth. The order of the Lbirth Vector matches the order of the Vector of cell id numbers (field ‘id’).

Length: cell array of vectors recording the cell length of each cell along their life cycle. Each entry of the cell array represents one cell as one vector of length as long as the number of frames in which this cell was detected. The order of the cell array entries matches the order of the array of cell id numbers (field ‘id’).

Frame: Same as the field ‘length’ but with the frame number at which the cell was detected. The vectors of frame numbers correspond to the vectors of cell length.

Cct: Vector of inter-division times, in frames, calculated as the time elapsed between the detected birth and the detected division.

gRate: Vector of relative growth rates (frame-1) calculated by fitting a linear model to the relation log(length)=f(time). The fitting step is made robust by excluding the data points that lay more than 2 standard deviations away from the mean of the residuals.

rmseFit: Vector of the root mean squared errors of the fit applied to calculate the growth rate based on the growth curve.

Rmsd: Vector of the root mean squared deviations of the logarithm of the ratios of two lengths measured consecutively. For each cell the vector of cell lengths is normalized by the length at birth (Li/L0). The logarithm of this normalized vector is differentiated (diff(log(Li/L0)) and the r.m.s.d. for this vector is computed and returned into the field ‘rmsd’.

This module converts the cellList format to a ".csv" format. The ".csv" format is a comma-delimited format that can be analyzed in Excel.

The structure of the ".csv" format is;

Title: The name and path of the file as well as the date of creation.

The parameters used for the cell contour detection are listed at the beginning of the file. Each parameter is reported on a new line starting with #.

$shiftframe: Reports the frame shifts, in pixels, from one image to the next, if computed prior to the analysis.

$cellListN: Reports the number of cells detected per frame.

%parameter values: Reports the values of each parameter for all cells in all frames. Each line (starting with #) refers to one detected cell; each parameter value is separated with a comma. In the case of a parameter represented by an array of values, these values appear separated by spaces. For an array that has more than one column, the different columns are separated by semicolon (;).
• Fame Number: Frame number in which the cell is detected
• Ancestors: Cell ID number of the mother cell, if any.
• Birthframe: Most useful in time lapses, this parameter records the frame number at which the cell was first detected.
• Box: An array of 4 values, in pixels, defining the bounding box of the cell. Use this values to crop the image and display this specific cell. The box parameter values are the same as in the *.mat format ([bottom, left, width, height]);
• Descendants: Cell ID number(s) of the detected descendants of this cell.
• Divisions: Frame at which a cell divides. This parameter value is useful in time lapse experiments and is filled in at the last frame at which a cell, as defined by its ID number, is detected.
• Mesh: An array of four columns, in pixels, specifying the location of the cell edges in image coordinates. As for the *.mat version, the mesh parameter (or field) is organized in 4 series of numbers (x1 y1 x2 y2). Series of numbers are separated by “;” while numbers within a series are space-separated. The vectors x1, y1 define one side of the cell while x2, y2 define the other side. Both half contours start and end at the same points ([x1(1),y1(1)] = [x2(1),y2(1)]).
• Length: Cell length in pixels
• Area: Cell area in pixels
• Polarity: Value defining the polarity of the cell.
• Signal0: Array of values, in arbitrary units, specifying the intensity profile along the cell length. The length of the vector has the same length as the cell mesh (x1, y1, x2 or y2) and each values corresponds to a cell segment defined by the cell mesh.



When spotDetection or objectDetection is used, extra fields of spots or objects are created in the cellList. The program will automatically check for the presence of these extra fields. If present, these fields will be exported to a comma-dilimited text file with headings spots or objects. However, the sub-fields are structured as semicolon dilimited as shown below;

• spots: [a1 a2 an; b1 b2 bn; ...], where numericals refer to the number of spots in a given cell and the alphabets refer to the sub-fields. The sub-fields are in this order; l, d, x, y, positions, and adj. Rsquared. See for more information.
• objects: [a1 a2 an; b1 b2 bn; ...], where numericals refer to the number of objects in a given cell and the alphabets refer to the sub-fields. The sub-fields are in this order; outlines, pixels, pixelvals, and area. The outlines sub-field is a 2-by-n array of sub-pixel location values. The first column refers to the x-locations while the second columns refers to y-locations, pixels are image unit values indicating location of nuleoids in image coordinates, pixelvals are the pixel values of each pixel location shown in pixels sub-field, and area sub-field is the calculated area of each nucleoid.

Text-format data generated through the High-throughput mode can be converted back to Matlab format. This is useful for those who want to perform post-processing on already processed image datasets in Matlab. Note: Make sure that, 'global cellList' is called in the Matlab command window.

In some circumstances when the ".out" file is large and does not need to be converted to cellList, the users have the option to go through the large data set and import chunks of data in to Matlab. There are different ways to do this and one suggestion would be to use the following command lines.