Re: Zeiss LSM Scan Type 2

Posted by Patrick Pirrotte on Aug 08, 2007; 8:50am
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-Scan-Type-2-tp3698595p3698598.html

Hi,

The version was not released yet. Meanwhile, I put a beta version of the
plugin here:

http://www.image-archive.org/typo3conf/ext/dam/mod_file/fileadmin/user_uploa
d/files_/LSM_Toolbox_4.0c/LSM_Toolbox.jar

It supports linescans and has a few bugfixes/improvements.

Best regards,

Patrick

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Philip
Ershler
Sent: 07 August 2007 06:47
To: [hidden email]
Subject: Re: Zeiss LSM Scan Type 2

Gentlemen,
        Was this new version of the LSM Toolbox ever released? I can't seem
to fine any reference to it.

Thank You,

Phil

On Apr 25, 2007, at 3:09 PM, jerome mutterer wrote:

> I'm sorry I haven't answered earlier.
> We have accumulated a number of bugfixes and a new version of LSM
> Toolbox is going to be released in the next 2 or three week. This
> version will support line scans as well, thanks to the cited report.
> Sincerely,
> Patrick and Jerome
>
>
> On 4/25/07, Philip Ershler <[hidden email]> wrote:
>>
>> 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
>>
>>
>>
>>