Re: Zeiss LSM Scan Type 2

Posted by Philip Ershler on Aug 08, 2007; 8:38pm
URL: http://imagej.273.s1.nabble.com/Zeiss-LSM-Scan-Type-2-tp3698595p3698599.html

Hello Patrick,
        The link below is not found on your server. I did start at www.image-
archive.org and found the LSM_Toolbox_4.00b_src.jar file. But Im  
afraid I don't know enough about Java to know how to compile the  
source. I certainly appreciate your efforts.

Thanks, Phil

On Aug 8, 2007, at 1:50 AM, Patrick Pirrotte wrote:

> 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
>>>
>>>
>>>
>>>