LOCI Bio-formats
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Dear users,
I used to open Deltavision files with the LOCI Bio-formats plugin. If I had 2 colors, the plugin would automatically open the image already colorized (and each channel could have been color balanced, etc, independently - even thought the 2 images of 2 different colors were in a same stack). For unknown reasons, I couldn't open the plugin, and further updated it -- the new version does not open the file in its colorized version. Any help would be appreciated. Thanks, Best wishes, Julien. -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Julien,
> I used to open Deltavision files with the LOCI Bio-formats plugin. If I had 2 colors, the plugin would automatically open the image already colorized (and each channel could have been color balanced, etc, independently - even thought the 2 images of 2 different colors were in a same stack). For unknown reasons, I couldn't open the plugin, and further updated it -- the new version does not open the file in its colorized version. Any help would be appreciated. Do you see an error message now? Or is it just that the images appear, but are not colorized? If the former, then please send the complete text of the error message. If the latter, could you please check that the "Color mode" option was set to "Colorized"? Regards, -Melissa On Thu, Sep 20, 2012 at 12:13:37AM +0000, Julien Vaubourgeix wrote: > Dear users, > > I used to open Deltavision files with the LOCI Bio-formats plugin. If I had 2 colors, the plugin would automatically open the image already colorized (and each channel could have been color balanced, etc, independently - even thought the 2 images of 2 different colors were in a same stack). For unknown reasons, I couldn't open the plugin, and further updated it -- the new version does not open the file in its colorized version. Any help would be appreciated. > > Thanks, > > Best wishes, Julien. > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Thanks for responding, Melissa.
There is no error message popping up --- previously, the image, colorized, used to appear with the n colors merged. The color mode option is set on default; I do not have the option to change it while the viewer stack ("View Stack with") chosen is ImageJ standard. Thanks for your help, Best wishes, Julien. On Sep 20, 2012, at 9:30 AM, Melissa Linkert wrote: > Hi Julien, > >> I used to open Deltavision files with the LOCI Bio-formats plugin. If I had 2 colors, the plugin would automatically open the image already colorized (and each channel could have been color balanced, etc, independently - even thought the 2 images of 2 different colors were in a same stack). For unknown reasons, I couldn't open the plugin, and further updated it -- the new version does not open the file in its colorized version. Any help would be appreciated. > > Do you see an error message now? Or is it just that the images appear, > but are not colorized? > > If the former, then please send the complete text of the error message. > If the latter, could you please check that the "Color mode" option was set > to "Colorized"? > > Regards, > -Melissa > > On Thu, Sep 20, 2012 at 12:13:37AM +0000, Julien Vaubourgeix wrote: >> Dear users, >> >> I used to open Deltavision files with the LOCI Bio-formats plugin. If I had 2 colors, the plugin would automatically open the image already colorized (and each channel could have been color balanced, etc, independently - even thought the 2 images of 2 different colors were in a same stack). For unknown reasons, I couldn't open the plugin, and further updated it -- the new version does not open the file in its colorized version. Any help would be appreciated. >> >> Thanks, >> >> Best wishes, Julien. >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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Hi Julien,
We highly advise the use of "Hyperstack" rather than "Standard ImageJ". The latter is a legacy mode that is not 5D nor composite aware. We actually removed it once but some users complained, so it is still there. If it still doesn't work with Hyperstack mode and Composite color mode, let us know. Regards, Curtis On Sep 20, 2012 7:30 PM, "Julien Vaubourgeix" <[hidden email]> wrote: > Thanks for responding, Melissa. > > There is no error message popping up --- previously, the image, colorized, > used to appear with the n colors merged. > > The color mode option is set on default; I do not have the option to > change it while the viewer stack ("View Stack with") chosen is ImageJ > standard. > > Thanks for your help, > > Best wishes, Julien. > > On Sep 20, 2012, at 9:30 AM, Melissa Linkert wrote: > > > Hi Julien, > > > >> I used to open Deltavision files with the LOCI Bio-formats plugin. If I > had 2 colors, the plugin would automatically open the image already > colorized (and each channel could have been color balanced, etc, > independently - even thought the 2 images of 2 different colors were in a > same stack). For unknown reasons, I couldn't open the plugin, and further > updated it -- the new version does not open the file in its colorized > version. Any help would be appreciated. > > > > Do you see an error message now? Or is it just that the images appear, > > but are not colorized? > > > > If the former, then please send the complete text of the error message. > > If the latter, could you please check that the "Color mode" option was > set > > to "Colorized"? > > > > Regards, > > -Melissa > > > > On Thu, Sep 20, 2012 at 12:13:37AM +0000, Julien Vaubourgeix wrote: > >> Dear users, > >> > >> I used to open Deltavision files with the LOCI Bio-formats plugin. If I > had 2 colors, the plugin would automatically open the image already > colorized (and each channel could have been color balanced, etc, > independently - even thought the 2 images of 2 different colors were in a > same stack). For unknown reasons, I couldn't open the plugin, and further > updated it -- the new version does not open the file in its colorized > version. Any help would be appreciated. > >> > >> Thanks, > >> > >> Best wishes, Julien. > >> > >> -- > >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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It's working very well --- thank you so much, Curtis.
And thanks to the community for always being extremely helpful. On Sep 20, 2012, at 8:37 PM, Curtis Rueden wrote: > Hi Julien, > > We highly advise the use of "Hyperstack" rather than "Standard ImageJ". The > latter is a legacy mode that is not 5D nor composite aware. We actually > removed it once but some users complained, so it is still there. > > If it still doesn't work with Hyperstack mode and Composite color mode, let > us know. > > Regards, > Curtis > On Sep 20, 2012 7:30 PM, "Julien Vaubourgeix" <[hidden email]> > wrote: > >> Thanks for responding, Melissa. >> >> There is no error message popping up --- previously, the image, colorized, >> used to appear with the n colors merged. >> >> The color mode option is set on default; I do not have the option to >> change it while the viewer stack ("View Stack with") chosen is ImageJ >> standard. >> >> Thanks for your help, >> >> Best wishes, Julien. >> >> On Sep 20, 2012, at 9:30 AM, Melissa Linkert wrote: >> >>> Hi Julien, >>> >>>> I used to open Deltavision files with the LOCI Bio-formats plugin. If I >> had 2 colors, the plugin would automatically open the image already >> colorized (and each channel could have been color balanced, etc, >> independently - even thought the 2 images of 2 different colors were in a >> same stack). For unknown reasons, I couldn't open the plugin, and further >> updated it -- the new version does not open the file in its colorized >> version. Any help would be appreciated. >>> >>> Do you see an error message now? Or is it just that the images appear, >>> but are not colorized? >>> >>> If the former, then please send the complete text of the error message. >>> If the latter, could you please check that the "Color mode" option was >> set >>> to "Colorized"? >>> >>> Regards, >>> -Melissa >>> >>> On Thu, Sep 20, 2012 at 12:13:37AM +0000, Julien Vaubourgeix wrote: >>>> Dear users, >>>> >>>> I used to open Deltavision files with the LOCI Bio-formats plugin. If I >> had 2 colors, the plugin would automatically open the image already >> colorized (and each channel could have been color balanced, etc, >> independently - even thought the 2 images of 2 different colors were in a >> same stack). For unknown reasons, I couldn't open the plugin, and further >> updated it -- the new version does not open the file in its colorized >> version. Any help would be appreciated. >>>> >>>> Thanks, >>>> >>>> Best wishes, Julien. >>>> >>>> -- >>>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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