cropping Z dimension
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ============================================================ Dear List Serv, I was wondering if anyone here knows of a way to crop free hand in the Z direction. For example im analyzing dendritic spines and it would be a lot easier to automate the process if i was able to eliminate branches that go off in the Z as i do not want to analyze that branch. A Z slice cropper would not suffice as it would crop part of the dendrite that I'm trying to analyze. The program i deconvolve with allows me to do a freehand crop in the XY however not in the Z(only box), thus the solution would probably be to mess with the dimensions temporarily so that the ZY or ZX becomes the XY however i don't know how to do this. Any ideas??? Your help is much appreciated. Thank You ------- Matiar Jafari |
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Dear Matiar, It is possible to do this using Imaris. You can use the Surfaces->Draw tab-->Contour tool to manually define a region which would be either included or excluded. You can choose the plane to draw the contours on, either XY, YZ, or XZ.
Then draw the desired contours and create the surface. You can then use the Surfaces-->Edit tab-->Mask All to mask the that drawn surface. In the "Mask Dataset" dialog, you can either duplicate the current channel or not - and then you seperately set the intensity of voxels inside and oustide of the surface to either the original value of that channel, or to an arbitrary value. Set the value to zero to crop out the desired region.
Please let me know if you need any further assistance. Best Regards, Arvonn Tully Technical and Application Support Western United States
Support Telephone:+1-888-332-4879 ext 12 fax: 866-691-9112 Bitplane, Inc.
Direct Line:+1-360-448-7599 On Wed, Sep 15, 2010 at 6:41 PM, Matiar Jafari <[hidden email]> wrote: ============================================================ |
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In reply to this post by Matiar Jafari
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To join, leave or search the confocal microscopy listserv, go to: http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy ============================================================ Matiar, You should be able to do this in ImageJ by free hand selecting the branch(s) you want to eliminate, selecting Edit->Clear, and just processing that slice. You would have to do this for each slice however but it should work. Dave Dave McDonald Scientific Imaging Lab Fred Hutchinson Cancer Research Center 1100 Fairview Avenue North, DE-512 Seattle, WA 98109 206-667-4205 http://www.fhcrc.org At 06:41 PM 9/15/2010, you wrote: >============================================================ >To join, leave or search the confocal microscopy listserv, go to: >http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy >============================================================ > >Dear List Serv, > >I was wondering if anyone here knows of a way to crop free hand in the >Z direction. For example im analyzing dendritic spines and it would >be a lot easier to automate the process if i was able to eliminate >branches that go off in the Z as i do not want to analyze that branch. > A Z slice cropper would not suffice as it would crop part of the >dendrite that I'm trying to analyze. The program i deconvolve with >allows me to do a freehand crop in the XY however not in the Z(only >box), thus the solution would probably be to mess with the dimensions >temporarily so that the ZY or ZX becomes the XY however i don't know >how to do this. Any ideas??? > >Your help is much appreciated. > >Thank You >------- >Matiar Jafari |
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In reply to this post by Matiar Jafari
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To join, leave or search the confocal microscopy listserv, go to:
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Hi Matiar If you have access to Imaris it is much better tu use their Filamentracer function to reconstructand quantify the whole tree and then select the branches you don't want to include in your final results. This way you can easily show to the referees what you did and why!! Good Luck eric
> Z direction. For example im analyzing dendritic spines and it would > be a lot easier to automate the process if i was able to eliminate > branches that go off in the Z as i do not want to analyze that branch. > A Z slice cropper would not suffice as it would crop part of the > dendrite that I'm trying to analyze. The program i deconvolve with > allows me to do a freehand crop in the XY however not in the Z(only > box), thus the solution would probably be to mess with the dimensions > temporarily so that the ZY or ZX becomes the XY however i don't know > how to do this. Any ideas??? > > Your help is much appreciated. > > Thank You > ------- > Matiar Jafari > |
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