I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended? Thanks for the help, -Brandon [cid:1b1e95a3-2efc-477f-925e-74b92b367f68] [cid:56f70b34-d199-466f-a578-76fde802d5ec] ____________________ Brandon Scott, PhD SDSMT, Nanoscience
Hi Brandon, There are at least a couple of parameters to try changing, 3D projection mode and dimTransparentVoxels. E.g. try either/both of the following: volume all projectionMode 3d vol all dimTransparentVoxels false See the “solid” volume rendering options and specifically these two settings for explanations. <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dispsolid> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#pmode> <http://rbvi.ucsf.edu/chimerax/docs/user/commands/volume.html#dimvox> This page about ChimeraX features for working with medical imaging data might also be of interest for anybody who is using the “solid” rendering style (on any type of data): <http://rbvi.ucsf.edu/chimerax/docs/user/dicom-quickref.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 15, 2019, at 9:18 AM, Scott, Brandon L. <Brandon.Scott@sdsmt.edu> wrote:
I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended?
Thanks for the help, -Brandon
<image3.png> <image2.png>
____________________ Brandon Scott, PhD SDSMT, Nanoscience <VolumeRotate.mp4>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Brandon, ChimeraX is displaying the volumetric rendering using a stack of xy planes -- when you view the planes edge on you don't see them. You can change this using the volume projection mode. volume #1 projectionMode 2d-xyz or volume #1 projectionMode 3d The default mode is 2d-z when showing a 3d image that is a thin slab (I think less than 5 to 1 aspect ratio). The 2d-xyz mode will show xy, yz, or xz planes depending on the view angle, and the 3d mode will use planes perpendicular to the view direction. The reason fo the multiple weird modes is that there are performance and quality tradeoffs, and which is the best mode depends on your data. Tom
On Mar 15, 2019, at 9:18 AM, Scott, Brandon L. wrote:
I am trying to set the thresholds to properly display volumetric fluorescence data, and for some reason, when viewed from the side, i.e. xz or yz projection, the volume goes black. I've attached two images (top view and side view) with not changes to anything else by positioning, and this can be seen clearly in the rotation video I attached. I guess my question is, is this a bug, or is it acting as it was intended?
Thanks for the help, -Brandon
<image3.png> <image2.png>
____________________ Brandon Scott, PhD SDSMT, Nanoscience <VolumeRotate.mp4>_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu <mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users <http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users>
participants (3)
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Elaine Meng -
Scott, Brandon L. -
Tom Goddard