To Open Metamorph Imaging System:

· Plug security key into the LPT1 port at the back of the computer.

· Open Metamorph (Start/Programs/Meta Imaging Series 4.0/Metamorph).

To Outline a Cell (or nucleus) using Metamorph:

· Once Metamorph is opened, use File/Open to open the picture of the cell you would like to outline.

· Adjust the contrast of the picture so that the cell can be clearly distinguished from the surroundings (to do this use the mouse on the contrast bar at the bottom left corner of the picture).

· Use the zoom button (top left of picture) to magnify the cell and make the edge of the membrane easy to determine.

· Open Microsoft Excel (if Excel is already open, it must be closed and opened again).

· In Metamorph, go under the Log menu and choose Open Data Log…

· When the Open Data Log box pops up, make sure the box next to Dynamic Data Exchange (DDE) is the only box checked. Click OK.

· The Export Log Data Box will then appear. It must have to following settings to work correctly:

Application: Other Application

Application Name: Excel

Topic Name: Sheet1 (If you want to log to another sheet in the spread sheet, enter the sheet's name here, ex Sheet2)

Item Name: R<r>C<c>

Starting Row: 1

Starting Column: 1

Click OK

· Under the Measure Menu, choose Track Points… (last choice).***

· ***In version 5.4r2, the Track Points option is under the Apps Menu.

· When the Track Points Box appears, change Source to Updating Image, and make sure that your image name appears on the line below. At the bottom of the box, for Table Statistics, choose Positions.

· Next, click the Config Log button. Under Parameter Configuration, double click until only X and Y have checks next to them. Then go to the Logging Options section and make sure both boxes are not checked. If you want to log all your data to a single line (x1 y1 x2 y2…) you can check the "Place data on current line" option BUT you cannot have more than 128 points, Excel will cut off part of your data (the max number of columns is 256). Click OK.

· Back in the Track Points box, click on the Add Track… button. Set the number of tracks to 1, Click OK.

· Begin clicking along the edge of the cell membrane, moving in a counter clockwise direction. Once the cell is outlined (about 150 points), click the Done button in the Track Points box.

· Click the "F9: Log Data" button in the Tracking Points box to transfer the points to Excel. Click "Clear All…" and clear the tracks.

· Close the cell picture, without saving changes.

· Go to Excel, and save the data As "Text (Tab Delimited) *.txt" type.

· If you choose not to close Excel now, you must close and then reopen your data log in Metamorph, and select a different sheet to log to (see "export log data" above).

· To outline another cell, repeat Outlining a Cell using Metamorph procedure.

If you have logged data in two columns, the following MatLab program will reformat it from

x1 y1

x2 y2

to x1 y1 x2 y2.

Before running this program, you must make sure that the save line (second to last line) will save the reformatted outline to the proper filename. You must save the changed m-file before running it in MatLab.

This program is located at: \\Engnt1\bme\Students\wonglab\Matlab\reformat_cell_outline.m

and

(wonglab2) C:\MATLABR11\work\reformat_cell_outline.m

%program for formatting Metamorph displacement data to correct form

clear

R=input( 'Press <CR> and input cell outline or nucleus file' )

[f,p]=uigetfile( '*.*' ) %user-interface brings up browse menu

cd (p) %changes directory

g = load (f)

gtmp2=g'

gtmp3=gtmp2(:)

gtmp4=gtmp3'

%[newmatfile, newpath] = uiputfile('*.txt', 'Save As')

path=p

% Change the name "outline.txt" to the name you want to save the reformated file as

save p0104c.txt gtmp4 -ascii

clear

This program draws the cell outline and the nucleus outline for a given cell. It uses the reformatted outline data (x1 y1 x2 y2) and should be used to make sure that the outline data agrees with the cell image.

The program prompts first for a cell's outline file, and then for the cell's nucleus outline file.

This program can be found at:

\\Engnt1\bme\Students\wonglab\Matlab\cell_outline.m

and

(wonglab2) C:\MATLABR11\work\cell_outline.m

%%%%%%%%%% Draw the cell outline %%%%%%%%%%

R=input( 'Press <CR> and input cell outline file' )

[f,p]=uigetfile( '*.*' ) %user-interface brings up browse menu

cd (p) %changes directory

celol=zeros(2,2*1024); % initialize cell outline vector to zero

celol = load (f); %read nonzero values from input file

xc=[celol(1:2:length(celol)),celol(1)]; % [Start,end]=[(Start:skip#:end),end]

yc=[-celol(2:2:length(celol)),-celol(2)]; %Defines x and y-values

%%%%%%%%%% Draw the cell nucleus outline %%%%%%%%%%

R=input( 'Press <CR> and input cell nucleus file' )

[f1,p1]=uigetfile( '*.*' )

cd (p1)

nucol=zeros(2,1024); % initialize the nucleus outline vector to zero

nucol =load (f1); % read non zero components from input file

xn=[nucol(1:2:length(nucol)),nucol(1)]; %see above

yn=[-nucol(2:2:length(nucol)),-nucol(2)]; %see above

%set the plotting axies to pixel units

xmin=0.0 ; xmax= +1300.0 ; ymin=-1300.0 ; ymax=0.0;

axis ([xmin xmax ymin ymax]); % add subsequent plots to the current axis system

hold on

plot(xn,yn, 'r' , 'linewidth' ,1.2);

hold on;

plot(xc,yc, 'g' , 'linewidth' ,1.2);

hold on