depth cue by color for tomogram
Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138
Hi Michael, Depth cueing is the closest to what you want in Chimera. If I make a map red, and then fade to blue at the back using depth cueing it does what you are asking for. I don’t understand what you mean by “real depth”. Depth cueing fades to a specified color as z values increase where z is measured perpendicular to your display screen. That seems to be exactly what is needed for the 3d glasses you describe. Tom
On Apr 15, 2015, at 11:52 PM, Michael Elbaum wrote:
Hello all,
I noticed a new sort of 3D color glasses (http://chromatek.com/ <http://chromatek.com/>) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses.
I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient.
thanks for any help, Michael
Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Tom, Thanks for the reply. With your example I managed to get the depth cue to work as you described. It took some playing with the Side View control. What I'd had in mind might better be called depth encoding. I want to color the top plane red and the bottom one blue with a gradient in between. That way I can explain that blue is in back and those with the glasses should see it correctly in 3D. If I turn the volume upside down the 3D would invert because it's really a static 2D scheme, but if I rock it slightly the colors would not be redrawn. Without the rocking, I see now that I can get the encoding effect using the depth cue and the Planes feature to set the limits. Chimera comes through again! best wishes, Michael ________________________________ From: Tom Goddard [goddard@sonic.net] Sent: Thursday, April 16, 2015 20:41 To: Michael Elbaum Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] depth cue by color for tomogram Hi Michael, Depth cueing is the closest to what you want in Chimera. If I make a map red, and then fade to blue at the back using depth cueing it does what you are asking for. I don’t understand what you mean by “real depth”. Depth cueing fades to a specified color as z values increase where z is measured perpendicular to your display screen. That seems to be exactly what is needed for the 3d glasses you describe. Tom [cid:58B7ECE0-7AEF-4661-9A9F-544246EB46D7@cgl.ucsf.edu] On Apr 15, 2015, at 11:52 PM, Michael Elbaum wrote: Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi. Refining my previous question: Is it possible to restrict & refresh depth cueing to the visible section rather than the global clipping planes? As it is, if I choose a section (either by Features > Planes) or by setting the clipping planes in Side View, the red/blue depth cue still represents the entire volume. I suppose I could crop and resave my dataset, but that seems a bit inflexible. Another question that arose in scripting commands is whether I can set clip, section, thickness by absolute slice number, as in the Volume Viewer GUI, rather than by relative scaled length. thanks, Michael ________________________________ From: Michael Elbaum Sent: Thursday, April 16, 2015 22:12 To: Tom Goddard Cc: chimera-users@cgl.ucsf.edu Subject: RE: [Chimera-users] depth cue by color for tomogram Hi Tom, Thanks for the reply. With your example I managed to get the depth cue to work as you described. It took some playing with the Side View control. What I'd had in mind might better be called depth encoding. I want to color the top plane red and the bottom one blue with a gradient in between. That way I can explain that blue is in back and those with the glasses should see it correctly in 3D. If I turn the volume upside down the 3D would invert because it's really a static 2D scheme, but if I rock it slightly the colors would not be redrawn. Without the rocking, I see now that I can get the encoding effect using the depth cue and the Planes feature to set the limits. Chimera comes through again! best wishes, Michael ________________________________ From: Tom Goddard [goddard@sonic.net] Sent: Thursday, April 16, 2015 20:41 To: Michael Elbaum Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] depth cue by color for tomogram Hi Michael, Depth cueing is the closest to what you want in Chimera. If I make a map red, and then fade to blue at the back using depth cueing it does what you are asking for. I don’t understand what you mean by “real depth”. Depth cueing fades to a specified color as z values increase where z is measured perpendicular to your display screen. That seems to be exactly what is needed for the 3d glasses you describe. Tom [cid:58B7ECE0-7AEF-4661-9A9F-544246EB46D7@cgl.ucsf.edu] On Apr 15, 2015, at 11:52 PM, Michael Elbaum wrote: Hello all, I noticed a new sort of 3D color glasses (http://chromatek.com/) that work via blue-red chromatic aberration rather than shifted pairs. I think this would be a useful addition if it isn't available already somehow. The major advantage for a lecture situation is that 2D images are visible also without glasses. I tried to encode depth by color in Chimera but was not successful. I'm using solid style with transparency to see "into" the tomogram, loaded in Volume Viewer. I'd like the deep features to be in one color and the higher parts another, with sparse regions relatively transparent. In the main Viewing panel there's an option for depth cue on the Effects tab, but the cueing is relative to the Side View orientation rather than the real depth. Also there seems to be no option for a color gradient. thanks for any help, Michael Prof Michael Elbaum Dept of Materials and Interfaces Weizmann Institute of Science Rehovot 76100, ISRAEL tel +972 (0)8-9343537 fax +972 (0)8-9344138 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Michael, There are additional parameters for the depth cueing, essentially where the “ramp” of shading starts and ends relative to the front and back global clipping planes, in scaled length. You can adjust them via GUI (go to the Effects tab in the same dialog as the Side View) or with commands “set dcStart” and “set dcEnd”, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#dccolor> The volume-planes displays as controlled by the Volume Viewer GUI are not via clipping but literally just displaying certain planes. To control via commands, see “volume” command planes options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes> However, since depth-cueing parameters are specified relative to the global clipping planes rather than in your dataset coordinates, it will probably require some fiddling to get them into the desired register. Besides mouse manipulation, you can use the “move” command for Z-translation. I sometimes prefer using “move” for more precise control, but it may be because of lack of coordination. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 16, 2015, at 2:24 PM, Michael Elbaum <michael.elbaum@weizmann.ac.il> wrote:
Hi. Refining my previous question: Is it possible to restrict & refresh depth cueing to the visible section rather than the global clipping planes? As it is, if I choose a section (either by Features > Planes) or by setting the clipping planes in Side View, the red/blue depth cue still represents the entire volume. I suppose I could crop and resave my dataset, but that seems a bit inflexible.
Another question that arose in scripting commands is whether I can set clip, section, thickness by absolute slice number, as in the Volume Viewer GUI, rather than by relative scaled length. thanks, Michael
From: Michael Elbaum Sent: Thursday, April 16, 2015 22:12 To: Tom Goddard Cc: chimera-users@cgl.ucsf.edu Subject: RE: [Chimera-users] depth cue by color for tomogram
Hi Tom,
Thanks for the reply. With your example I managed to get the depth cue to work as you described. It took some playing with the Side View control.
What I'd had in mind might better be called depth encoding. I want to color the top plane red and the bottom one blue with a gradient in between. That way I can explain that blue is in back and those with the glasses should see it correctly in 3D. If I turn the volume upside down the 3D would invert because it's really a static 2D scheme, but if I rock it slightly the colors would not be redrawn.
Without the rocking, I see now that I can get the encoding effect using the depth cue and the Planes feature to set the limits. Chimera comes through again!
best wishes, Michael
Hi Elaine, Thanks for your reply and your helpful suggestions. I succeeded to make something presentable, though not what I'd had in mind. I showed a rocking volume instead. The red/blue by depth 3D works well. I can make a stack of visible slices move up through a larger reconstructed tomographic volume in "solid" mode. I had wanted to maintain the red/blue cueing at each step through the stack. the set dcStart and dcEnd commands are not "movie-related", so it seems that I should write a script imposing a new value to each and then update the visible section position iteratively per move, i.e. a long list rather than a loop. (That was more than I could do under time pressure before a talk.) Perhaps I can find a way to generate a suitable script automatically. thanks for your help, Michael ________________________________________ From: Elaine Meng [meng@cgl.ucsf.edu] Sent: Sunday, May 17, 2015 02:35 To: Michael Elbaum Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] depth cue by color for tomogram Hi Michael, There are additional parameters for the depth cueing, essentially where the “ramp” of shading starts and ends relative to the front and back global clipping planes, in scaled length. You can adjust them via GUI (go to the Effects tab in the same dialog as the Side View) or with commands “set dcStart” and “set dcEnd”, see: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/sideview.html#effects> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/set.html#dccolor> The volume-planes displays as controlled by the Volume Viewer GUI are not via clipping but literally just displaying certain planes. To control via commands, see “volume” command planes options: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#planes> However, since depth-cueing parameters are specified relative to the global clipping planes rather than in your dataset coordinates, it will probably require some fiddling to get them into the desired register. Besides mouse manipulation, you can use the “move” command for Z-translation. I sometimes prefer using “move” for more precise control, but it may be because of lack of coordination. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/move.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On May 16, 2015, at 2:24 PM, Michael Elbaum <michael.elbaum@weizmann.ac.il> wrote:
Hi. Refining my previous question: Is it possible to restrict & refresh depth cueing to the visible section rather than the global clipping planes? As it is, if I choose a section (either by Features > Planes) or by setting the clipping planes in Side View, the red/blue depth cue still represents the entire volume. I suppose I could crop and resave my dataset, but that seems a bit inflexible.
Another question that arose in scripting commands is whether I can set clip, section, thickness by absolute slice number, as in the Volume Viewer GUI, rather than by relative scaled length. thanks, Michael
From: Michael Elbaum Sent: Thursday, April 16, 2015 22:12 To: Tom Goddard Cc: chimera-users@cgl.ucsf.edu Subject: RE: [Chimera-users] depth cue by color for tomogram
Hi Tom,
Thanks for the reply. With your example I managed to get the depth cue to work as you described. It took some playing with the Side View control.
What I'd had in mind might better be called depth encoding. I want to color the top plane red and the bottom one blue with a gradient in between. That way I can explain that blue is in back and those with the glasses should see it correctly in 3D. If I turn the volume upside down the 3D would invert because it's really a static 2D scheme, but if I rock it slightly the colors would not be redrawn.
Without the rocking, I see now that I can get the encoding effect using the depth cue and the Planes feature to set the limits. Chimera comes through again!
best wishes, Michael
participants (3)
-
Elaine Meng -
Michael Elbaum -
Tom Goddard