Zeiss LSM Scan Type 2
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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: (801) 230-8771 alt ph: (801) 587-9528 fax: (801) 581-3128 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: (801) 230-8771 alt ph: (801) 587-9528 fax: (801) 581-3128 e-mail: [hidden email] |
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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 > > > > Philip R. Ershler Ph.D. > University of Utah > Cardiovascular Research and Training Institute > 95 South 2000 East > Salt Lake City, UT 84112-5000 > > phone: (801) 230-8771 > alt ph: (801) 587-9528 > fax: (801) 581-3128 > 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: (801) 230-8771 > alt ph: (801) 587-9528 > fax: (801) 581-3128 > e-mail: [hidden email] > |
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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 >> >> >> >> |
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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 >> >> >> >> |
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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 >>> >>> >>> >>> |
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Hi Philip,
Somehow I bugged the url. This should work: http://www.image-archive.org/fileadmin/user_upload/files_/LSM_Toolbox_4.0c/L SM_Toolbox.jar Best regards, Patrick -----Original Message----- From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Philip Ershler Sent: 08 August 2007 21:38 To: [hidden email] Subject: Re: Zeiss LSM Scan Type 2 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 >>> >>> >>> >>> |
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Hi Patrick,
Thank you for the beta version of LSM Toolbox. At least for my purposes it works just beautifully! I would like to propose a feature request, if I may. In addition to being able to dump the time stamps to a text file, it would be wonderful to be able to also dump the time stamps for the markers to a text file. Once again, thank you for all your efforts on this plugin. Phil On Aug 9, 2007, at 3:38 AM, Patrick Pirrotte wrote: > Hi Philip, > > Somehow I bugged the url. This should work: > http://www.image-archive.org/fileadmin/user_upload/files_/ > LSM_Toolbox_4.0c/L > SM_Toolbox.jar > > Best regards, > > Patrick > > -----Original Message----- > From: ImageJ Interest Group [mailto:[hidden email]] On Behalf > Of Philip > Ershler > Sent: 08 August 2007 21:38 > To: [hidden email] > Subject: Re: Zeiss LSM Scan Type 2 > > 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 >>>> >>>> >>>> >>>> |
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