Zeiss LSM Scan Type 2

Posted by Philip Ershler on Apr 25, 2007; 9:43pm
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-Scan-Type-2-tp3698595.html

I guess this is really a question for Wayne.

I am trying to deal with linescan images that come from a Zeiss LSM  
510 confocal. Initially, when I tried to open a linescan file with  
either LSM_Reader or the LSM_Toolbox, I got a message

Unsupported LSM scantype: 2

        So I got the source for LSM_Reader Plug In and added the following  
code to the switch for case 2: in LSM_Reader.java.

                ImagePlus[] imps = null;
                switch (cz.ScanType) {
                case 0:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                case 1:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                case 2:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                case 3:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                case 4:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                case 5:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                case 6:
                        imps = readStack(stream, lsmFi, cz, thumb);
                        return imps;
                default:
                        if (verbose)
                                IJ.error("Unsupported LSM svvcantype: " + cz.ScanType);
                        break;
                }
                return imps;

        Now the LSM_Reader Plug In seems to open the LSM linescan files  
without problem. It would be very useful if linescan files could be  
opened from the LSM_Toolbox. I understand from the web site run by  
[hidden email] and [hidden email]  
that the LSM_Toolbox uses a version of LSM_Reader that has been  
integrated in ImageJ. Is there any chance that the above patch could  
be included in the integrated LSM_Reader? I have sent e-mail to  
[hidden email] and [hidden email]  
(who have very kindly written the Zeiss LSM support). As of yet, I  
have not heard back.

Thank You,

Phil



Philip R. Ershler Ph.D.
University of Utah
Cardiovascular Research and Training Institute
95 South 2000 East
Salt Lake City, UT 84112-5000

phone: [phone]
alt ph: [phone]
fax: [phone]
e-mail: [hidden email]


Philip R. Ershler Ph.D.
University of Utah
Cardiovascular Research and Training Institute
95 South 2000 East
Salt Lake City, UT 84112-5000

phone: [phone]
alt ph: [phone]
fax: [phone]
e-mail: [hidden email]