Dear all, I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series? Regards, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk@ut.ee phone: 58244846
Hi Arto, The coloring of a volume series using Segment Map (ie Segger) color by region disappears when you play a volume series because the volume series code removes each surface after it undisplays it. Then when it recomputes the surface the next time it is displayed the coloring is gone. There is a Volume Series panel option "Cache [N] renderings" that tells it to keep up to N surfaces. Just set N to 10 or more and the surfaces won't be removed and the coloring will be preserved. The vseries command also has that option. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volseries/volserie... The reason the volume series surfaces are removed is because this is typically used with 3D light microscopy time series with hundreds of time points where you will run out of memory if all surfaces are kept. Some coloring methods can restore the coloring if the surface changes or is removed and recalculated (like color zone, or color by volume data value). Those coloring methods have coded the ability to recompute the coloring. The Segment Map (aka Segger) tool does not do that (it was written outside our lab and the recolor involves some more complex code). Tom
On Jan 25, 2021, at 3:21 AM, Arto Pulk <arto.pulk@ut.ee> wrote:
Dear all,
I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series?
Regards, Arto
Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk@ut.ee <mailto:arto.pulk@ut.ee> phone: 58244846
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Hey, Tom Thank you, the Cache N rendering indeed preserves, the surface coloring of the Segmented map coloring sceme. Best, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk@ut.ee phone: 58244846 ________________________________ From: Tom Goddard <goddard@sonic.net> Sent: Monday, January 25, 2021 9:35 PM To: Arto Pulk <arto.pulk@ut.ee> Cc: chimera-users@cgl.ucsf.edu <chimera-users@cgl.ucsf.edu> Subject: Re: [Chimera-users] coloring the volume series Hi Arto, The coloring of a volume series using Segment Map (ie Segger) color by region disappears when you play a volume series because the volume series code removes each surface after it undisplays it. Then when it recomputes the surface the next time it is displayed the coloring is gone. There is a Volume Series panel option "Cache [N] renderings" that tells it to keep up to N surfaces. Just set N to 10 or more and the surfaces won't be removed and the coloring will be preserved. The vseries command also has that option. https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volseries/volserie... The reason the volume series surfaces are removed is because this is typically used with 3D light microscopy time series with hundreds of time points where you will run out of memory if all surfaces are kept. Some coloring methods can restore the coloring if the surface changes or is removed and recalculated (like color zone, or color by volume data value). Those coloring methods have coded the ability to recompute the coloring. The Segment Map (aka Segger) tool does not do that (it was written outside our lab and the recolor involves some more complex code). Tom On Jan 25, 2021, at 3:21 AM, Arto Pulk <arto.pulk@ut.ee<mailto:arto.pulk@ut.ee>> wrote: Dear all, I would like to make a movie using volume series. I have 10 maps (from Relion) that I upload to volume series. Now I would like to color the moving parts of the map. One can use zone coloring, but it does not do the precise job to color specific volumes of the map as it is radius specific. Then there is "surface coloring" by "volume data value". I can make a mask and color the mask region, but it makes the color gradient and I do not have control of the region outside of the mask at it will be mixture of colors. The best way to color is to use "segment map" and then go to "Regions" and "color density map". It does good job to color specific map volumes but the colors are not permanent. If you Play the Volme Series then colors vanish. So, is there any good way to color Volume Series? Regards, Arto Institute of Technology University of Tartu Nooruse 1 50411, Tartu Estonia Dr. Arto Pulk email: arto.pulk@ut.ee<mailto:arto.pulk@ut.ee> phone: 58244846 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
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Arto Pulk -
Tom Goddard