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
loadimagestack commands, e.g.:
<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,
'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
- '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
- 'border' - border around the cell in pixels. Set <0 to use standard
- '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
- '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.