Deltavision file format
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Hi,
Just wondered whether anyone else had noticed the disconnect between the deltavision microscopes SoftWorx software used to acquire/open/analyse deltavision files and imageJ with respect to image orientation. Whenever I open a deltavision file, either with the ImageJ open command, or LOCI bioformats importer, I have to do "edit > transform > flip vertically" because imageJ opens my deltavision files upside down from how they are displayed in Applied precisions SoftWorx software. Just wondered whether others also have this "problem" with deltavision files... and whether its worth mentioning for a "fix"... or whether there is a reason for opening deltavision files in this orientation? Thanks Mike __________ Information from ESET Smart Security, version of virus signature database 5444 (20100912) __________ The message was checked by ESET Smart Security. http://www.eset.com |
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Yes, I have this same problem. I don't use ImageJ as a rule so I have not been much put out by it. It would be a major pain if ImageJ is the program of choice though. Worth a request.
However, if you do all you .dv files in ImageJ what would be the difference? Aurelie Snyder ________________________________________ From: ImageJ Interest Group [[hidden email]] On Behalf Of Michael Cundell [[hidden email]] Sent: Sunday, September 12, 2010 9:39 AM To: [hidden email] Subject: Deltavision file format Hi, Just wondered whether anyone else had noticed the disconnect between the deltavision microscopes SoftWorx software used to acquire/open/analyse deltavision files and imageJ with respect to image orientation. Whenever I open a deltavision file, either with the ImageJ open command, or LOCI bioformats importer, I have to do "edit > transform > flip vertically" because imageJ opens my deltavision files upside down from how they are displayed in Applied precisions SoftWorx software. Just wondered whether others also have this "problem" with deltavision files... and whether its worth mentioning for a "fix"... or whether there is a reason for opening deltavision files in this orientation? Thanks Mike __________ Information from ESET Smart Security, version of virus signature database 5444 (20100912) __________ The message was checked by ESET Smart Security. http://www.eset.com |
Re: Deltavision file format
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In reply to this post by Mike A
Hi Mike,
sometimes we have noticed similar things. To get this fixed, please send to Curtis and Melissa of the bio-formats file reader team an example of a misbehaving file... they are cc'd to this email. only with concrete examples in the hands of the software developers can these little but annoying problems be solved! cheers Dan Begin forwarded message: > ate: Sun, 12 Sep 2010 17:39:17 +0100 > From: Michael Cundell <[hidden email]> > Subject: Deltavision file format > > Hi, > > Just wondered whether anyone else had noticed the disconnect between the deltavision microscopes SoftWorx software used to acquire/open/analyse deltavision files and imageJ with respect to image orientation. Whenever I open a deltavision file, either with the ImageJ open command, or LOCI bioformats importer, I have to do "edit > transform > flip vertically" because imageJ opens my deltavision files upside down from how they are displayed in Applied precisions SoftWorx software. > > Just wondered whether others also have this "problem" with deltavision files... and whether its worth mentioning for a "fix"... or whether there is a reason for opening deltavision files in this orientation? > > Thanks > > Mike Dr. Daniel James White BSc. (Hons.) PhD Senior Microscopist / Image Visualisation, Processing and Analysis Light Microscopy and Image Processing Facilities Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstrasse 108 01307 DRESDEN Germany +49 (0)15114966933 (German Mobile) +49 (0)351 210 2627 (Work phone at MPI-CBG) +49 (0)351 210 1078 (Fax MPI-CBG LMF) http://www.bioimagexd.net BioImageXD http://pacific.mpi-cbg.de Fiji - is just ImageJ (Batteries Included) http://www.chalkie.org.uk Dan's Homepages https://ifn.mpi-cbg.de Dresden Imaging Facility Network dan (at) chalkie.org.uk ( white (at) mpi-cbg.de ) |
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In reply to this post by Aurelie Snyder
I did contemplate whether to bother mentioning it or not given the fact that
i can just do image > transform > flip vertically. Just wanted to bring it to attention really. Orientation doesnt really matter for fluorescence... however if you have differential interferance contrast/nomaski light images then the polarisation appears to come from the wrong direction when the file is opened in imageJ... so if you want to process images for presentation then you have to flip in imageJ at some point. Mike -------------------------------------------------- From: "Aurelie Snyder" <[hidden email]> Sent: Sunday, September 12, 2010 8:43 PM To: <[hidden email]> Subject: Re: Deltavision file format > Yes, I have this same problem. I don't use ImageJ as a rule so I have not > been much put out by it. It would be a major pain if ImageJ is the > program of choice though. Worth a request. > However, if you do all you .dv files in ImageJ what would be the > difference? > > > Aurelie Snyder > > ________________________________________ > From: ImageJ Interest Group [[hidden email]] On Behalf Of Michael > Cundell [[hidden email]] > Sent: Sunday, September 12, 2010 9:39 AM > To: [hidden email] > Subject: Deltavision file format > > Hi, > > Just wondered whether anyone else had noticed the disconnect between the > deltavision microscopes SoftWorx software used to acquire/open/analyse > deltavision files and imageJ with respect to image orientation. Whenever > I open a deltavision file, either with the ImageJ open command, or LOCI > bioformats importer, I have to do "edit > transform > flip vertically" > because imageJ opens my deltavision files upside down from how they are > displayed in Applied precisions SoftWorx software. > > Just wondered whether others also have this "problem" with deltavision > files... and whether its worth mentioning for a "fix"... or whether there > is a reason for opening deltavision files in this orientation? > > Thanks > > Mike > > > __________ Information from ESET Smart Security, version of virus > signature database 5444 (20100912) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > > > __________ Information from ESET Smart Security, version of virus > signature database 5447 (20100913) __________ > > The message was checked by ESET Smart Security. > > http://www.eset.com > > > __________ Information from ESET Smart Security, version of virus signature database 5447 (20100913) __________ The message was checked by ESET Smart Security. http://www.eset.com |
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Hi Mike,
Thanks for the bug report. I'll second Dan's suggestion: if you email us (the Bio-Formats developers) with a sample file, we can get it fixed. For files ~15MB or less, email attachments are fine; for larger files let us know if you need a place to upload data. You can find contact information here: http://www.loci.wisc.edu/software/mailing-lists Thanks, Curtis On Mon, Sep 13, 2010 at 10:57 AM, Michael Cundell <[hidden email]>wrote: > I did contemplate whether to bother mentioning it or not given the fact > that i can just do image > transform > flip vertically. Just wanted to > bring it to attention really. Orientation doesnt really matter for > fluorescence... however if you have differential interferance > contrast/nomaski light images then the polarisation appears to come from the > wrong direction when the file is opened in imageJ... so if you want to > process images for presentation then you have to flip in imageJ at some > point. > > Mike > > -------------------------------------------------- > From: "Aurelie Snyder" <[hidden email]> > Sent: Sunday, September 12, 2010 8:43 PM > > To: <[hidden email]> > Subject: Re: Deltavision file format > > Yes, I have this same problem. I don't use ImageJ as a rule so I have not >> been much put out by it. It would be a major pain if ImageJ is the program >> of choice though. Worth a request. >> However, if you do all you .dv files in ImageJ what would be the >> difference? >> >> >> Aurelie Snyder >> >> ________________________________________ >> From: ImageJ Interest Group [[hidden email]] On Behalf Of Michael >> Cundell [[hidden email]] >> Sent: Sunday, September 12, 2010 9:39 AM >> To: [hidden email] >> Subject: Deltavision file format >> >> Hi, >> >> Just wondered whether anyone else had noticed the disconnect between the >> deltavision microscopes SoftWorx software used to acquire/open/analyse >> deltavision files and imageJ with respect to image orientation. Whenever I >> open a deltavision file, either with the ImageJ open command, or LOCI >> bioformats importer, I have to do "edit > transform > flip vertically" >> because imageJ opens my deltavision files upside down from how they are >> displayed in Applied precisions SoftWorx software. >> >> Just wondered whether others also have this "problem" with deltavision >> files... and whether its worth mentioning for a "fix"... or whether there is >> a reason for opening deltavision files in this orientation? >> >> Thanks >> >> Mike >> >> >> __________ Information from ESET Smart Security, version of virus >> signature database 5444 (20100912) __________ >> >> The message was checked by ESET Smart Security. >> >> http://www.eset.com >> >> >> __________ Information from ESET Smart Security, version of virus >> signature database 5447 (20100913) __________ >> >> >> The message was checked by ESET Smart Security. >> >> http://www.eset.com >> >> >> >> > __________ Information from ESET Smart Security, version of virus signature > database 5447 (20100913) __________ > > > The message was checked by ESET Smart Security. > > http://www.eset.com > |
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