This function displays the cells from a microscope image with the cells detected on this image and spots inside, cropped and displayed on a grid (the dimensions can be regulated). The cells and the spots to be displayed can be filtered using several criteria.

  • <cellList> - an array that contains meshes. You can drag and drop the file with the data into MATLAB workspace or open it using MATLAB Import Tool. The default name of the variable is cellList, but it can be renamed.
  • <images> - a 3D array of images. It can be obtained using loadimageseries and loadimagestack commands, e.g.: images=loadimageseries('c:\users\test\imagefiles',1);
  • <framelist> - list of frames to display, i.e. [1 3 4 10] to display frames 1, 3, 4, and 10. Default: all frames.
  • <spotfieldname> - name of the field containing spots, must start with 'spots', e.g. 'spots', 'spots1', 'spots2', etc. Default: 'spots'. Set the fieldnames to an unexisting field to display cell outlines, but not spots, e.g. dispcellgrid(cellList,images,1,0,'spotsx').
  • 'numbers' - use this option to display the numbers inside cells.
  • 'disk' - display spots as filled disks rather than dots. The radius in this case is measured in image pixels, not screen points.
  • 'circle' - display a circle instead of a filled disk.

The rest of the parameters must be submitted in the format <parametername>,<parametervalue>, where <parametername> must be in quotes and <parametervalue> must be the value of this parameter. For example: dispcellall(cellList,images,cell,'markersize',2). Here are the possible parameters:

  • 'markersize' - spots marker size, 0 - don't show, default automatic.
  • 'imagelimits' - image scaling limits, default max to min.
  • 'colortable' - nx3 table of the marker disk colors. The table is an n-by-3 or n+1-by-3 matrix, where n if the number of fields. Each row corresponds to the color of the field, in the RGB (red, green, blue) format, the optional extra row corresponds to the color of overlapping regions.
  • 'border' - border around the cell in pixels. Set <0 to use standard box.
  • 'dimensions' - dimensions of the 'grid' to display: [#rows #colums].

Filtering parameters: only cells/spots satisfying them will be displayed. If no spot exists in the cell or should bedisplayed and any of the spot filters is used, the cell will only be displayed if 'nspots' parameter is present and contains zero.

  • 'cellintensity' - array of two numbers: low and high limits of the total intensity in the cell (as written in the mesh - either <spotfieldname> field or, if not provided, 'signal1' field)
  • 'cellmeanintensity' - mean intensity in the cell
  • 'celllength' - low and high limits of the cell length (in pixels)
  • 'cellarea' - low and high limits of the cell area (in pixels squared)
  • 'cellvolume' - low and high limits of the cell volume (in pixels cubic)
  • 'cellmeanwidth' - low and high limits of the mean (along the length) width of the cell
  • 'cellmaxwidth' - low and high limits of the maximum width of the cell
  • 'cellcurvature' - low and high limits of the cell curvature (in 1/pixel)
  • 'nspots' - list of possible numbers of spots (e.g. 0:3 for up to 3 spots)
  • 'spotmagnitude' - low and high limits of the spot magnitude
  • 'spotheight' - low and high limits of the spot height (intensity units)
  • 'spotwidth' - low and high limits of the spot width (in pixels)
  • 'spotposition' - low and high limits of the spot position from the "old" pole of the cell. This parameter allows more than 2 limits, in which case the spot will be displayed if it is either between 1st and 2nd, or 3rd and 4th, etc.
  • 'spotrelposition' - low and high limits of the relative (between 0 and 1) spot position, measured from the "lod" pole. This parameter also allows more than two limits.