dispcellall
Syntax:
dispcellall(cellList,images)
dispcellall(cellList,images,framelist)
dispcellall(cellList,images,...,spotfieldname)
dispcellall(cellList,images,...,spotfieldname1,spotfieldname2,spotfieldname3)
dispcellall(cellList,images,...,signalfieldname)
dispcellall(cellList,images,...,'numbers')
dispcellall(cellList,images,...,'disk')
dispcellall(cellList,images,...,'circle')
This function displays a microscope image with the cells detected on this image and spots inside (if present). The cells and the spots to be displayed can be filtered using several criteria.
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:
Filtering parameters: only cells/spots satisfying them will be displayed. If no spot exists in the cell or should be displayed and any of the spot filters is used, the cell will only be displayed if 'nspots' parameter is present and contains zero.
This example demonstrates how to use some of the display options of the dispspotall command. It uses images of C. crescentus CB15N cells expressing CFP-ParB and PopZ-YFP chimeric proteins (courtesy of Dr. Geraldine Laloux).
1. Start MATLAB. Set the working path in MATLAB to the folder of the example: ...\MicrobeTracker...\examples\spotfinder2.
2. Load the cb15nparbpopz.mat file by dragging- and-dropping it into the MATLAB's workspace.
If you with, you can obtain this file yourself. For this, start MicrobeTracker. Load the default parameter set alg4.set. Load the phase contrast image by checking the Stack checkbox, then clicking on the Load phase button and selecting the ...\cb15nparbpopz\phase.tif file. Click the All frames to do detection. Save the resulting file on the disk. Close MicrobeTracker and start SpotFinderZ. Run Adjust regime, load the ...\cb15nparbpopz\cfp.tif file and go through several cells selecting the right spots, then click Stop. Select checkboxes Meshes and File, then click Run selecting the input and output file. Repeat the same procedure for the ...\cb15nparbpopz\yfp.tif with loading the meshes file just generated by SpotFinderZ, except for changing the Field value to "spots2" (this will create different fields for CFP anf YFP spots). Save to the same file. Close SpotFinderZ and load the file into MATLAB's workspace.
3. Load the images we will need using the loadimagestack function.
cfp=loadimagestack('cb15parbpopz\cfp.tif');
yfp=loadimagestack('cb15parbpopz\yfp.tif');
4. Now run the dispcellall function with the default parameters to display the CFP spots overlaying the corresponding image:
dispcellall(cellList,cfp)
5. To display the YFP spots change the field to display from the default "spots" to "spots2":
dispcellall(cellList,yfp,'spots2')
6. Now display the two types of spots together without any background image:
dispcellall(cellList,[],'spots','spots2')
7. Now display the two types of spots together, but using filled circles instead of dots. This regime is useful to see overlapping spots. Let's also change the radius of the spots from the default of 1.5 pixels to 2.5 pixels. Zoom the image after plotting to see the details better:
dispcellall(cellList,[],'spots','spots2','disk','markersize',2.5)
8. The way disks are displayed can be modified by the user by directly supplying their colors. The color table is an n-by-3 or n+1-by-3 matrix, where n if the number of fields (two in our case - "spots" and "spots2"). Each row corresponds to the color of the field, in the RGB (red, green, blue) format e.g. for magenta and blue colors the matrix is:
[1 0 1; 0 0 1]
The optional last row correspond to the merge color if two or more different spots overlap. Let's display the spots with yellow and blue colors without merge:
dispcellall(cellList,[],'spots','spots2','disk','markersize',2.5,'colortable',[1 1 0;0 0 1])
Top pages: MicrobeTracker Tools, MicrobeTracker Suite.