Volume and mesh data simultaneously? Coordinate space is different
Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap). Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh? (this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>) Thanks a lot in advance, Marvin
Hi Marvin, That link asks for a login, but I can imagine you have two representations of the same object(s) that are not superimposed. (BTW, you can attach images to emails here as long as they aren’t huge.) …However, I don’t understand where these files came from, and thus why you expect them to be aligned. Did you read a TIFF stack into Chimera as a volume, then contour it, and then export the surface as .wrl? Chimera does not save volumes as .tif, it only saves an image of the graphics window contents in that format, without relationship to the original 3D coordinates. If some other program wrote the .tif (stack??) and .wrl, I’d put the onus on that program to preserve the coordinate system. Or, maybe it is not possible to preserve 3D coordinates with the .tif format and you’d have to use a real volume format instead of an image stack. I’m not the expert on this topic, but the others are away. We may need to wait for their opinion(s), but in the meanwhile, clarifying your workflow might help. Thanks, 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 Jul 27, 2016, at 9:49 AM, Marvin Albert <marvin.albert@gmail.com> wrote:
Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap).
Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh?
(this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3)
Thanks a lot in advance, Marvin
Hi Elaine, ok I attached the files here. I have an image processing pipeline (external to chimera) which segments 3d image stacks and produces a .wrl file (also including meshlab as a tool). I want to use chimera for producing a nice video visualising the individual steps of the segmentation (which consist of .tif and .wrl outputs). If I load in the .wrl and .tif into python for example, coordinates perfectly overlap. Also the coordinates in the raw .wrl file seem to look good. How does chimera load in the 3d tif stacks? With kind regards, Marvin
On 27 Jul 2016, at 19:14, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Marvin, That link asks for a login, but I can imagine you have two representations of the same object(s) that are not superimposed. (BTW, you can attach images to emails here as long as they aren’t huge.)
…However, I don’t understand where these files came from, and thus why you expect them to be aligned. Did you read a TIFF stack into Chimera as a volume, then contour it, and then export the surface as .wrl? Chimera does not save volumes as .tif, it only saves an image of the graphics window contents in that format, without relationship to the original 3D coordinates.
If some other program wrote the .tif (stack??) and .wrl, I’d put the onus on that program to preserve the coordinate system. Or, maybe it is not possible to preserve 3D coordinates with the .tif format and you’d have to use a real volume format instead of an image stack.
I’m not the expert on this topic, but the others are away. We may need to wait for their opinion(s), but in the meanwhile, clarifying your workflow might help. Thanks, 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 Jul 27, 2016, at 9:49 AM, Marvin Albert <marvin.albert@gmail.com> wrote:
Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap).
Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh?
(this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3)
Thanks a lot in advance, Marvin
Hi Marvin, Thanks for attaching the files. I don’t know the details of how the coordinates are set up for the TIF stack, so that may have to wait until next week when our Volume Viewer expert is back from vacation. However, in the meanwhile... After opening your data, it occurred to me that in Volume Viewer you may be able to change the offset (origin grid index) and voxel size of the volume data to sync up with the VRML model. In the Volume Viewer menu, choose Features… Coordinates. That will put the relevant entry fields in the Volume Viewer dialog. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates> You can also make these adjustments using options of the “volume” command instead of interactively in the Volume Viewer dialog. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/volume.html#dimensions> I guess the main difficulty is figuring out what those values should be, but maybe you already know. 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 Jul 28, 2016, at 12:55 AM, Marvin Albert <marvin.albert@gmail.com> wrote:
Hi Elaine,
ok I attached the files here.
I have an image processing pipeline (external to chimera) which segments 3d image stacks and produces a .wrl file (also including meshlab as a tool). I want to use chimera for producing a nice video visualising the individual steps of the segmentation (which consist of .tif and .wrl outputs). If I load in the .wrl and .tif into python for example, coordinates perfectly overlap. Also the coordinates in the raw .wrl file seem to look good.
How does chimera load in the 3d tif stacks?
With kind regards, Marvin
<cube.tif><cube.wrl>
On 27 Jul 2016, at 19:14, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi Marvin, That link asks for a login, but I can imagine you have two representations of the same object(s) that are not superimposed. (BTW, you can attach images to emails here as long as they aren’t huge.)
…However, I don’t understand where these files came from, and thus why you expect them to be aligned. Did you read a TIFF stack into Chimera as a volume, then contour it, and then export the surface as .wrl? Chimera does not save volumes as .tif, it only saves an image of the graphics window contents in that format, without relationship to the original 3D coordinates.
If some other program wrote the .tif (stack??) and .wrl, I’d put the onus on that program to preserve the coordinate system. Or, maybe it is not possible to preserve 3D coordinates with the .tif format and you’d have to use a real volume format instead of an image stack.
I’m not the expert on this topic, but the others are away. We may need to wait for their opinion(s), but in the meanwhile, clarifying your workflow might help. Thanks, 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 Jul 27, 2016, at 9:49 AM, Marvin Albert <marvin.albert@gmail.com> wrote:
Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap).
Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh?
(this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3)
Thanks a lot in advance, Marvin
Hi Marvin, Your cube.tif file is a stack of 30 images each 50 by 40 pixels. So Chimera displayed it with x, y, and z ranges of 0-50, 0-40, and 0-30. Your VRML file cube.vrml has a cube with x, y, z values ranging from 5-9, 10-14, 15-19. How would you expect these two data sets to align in Chimera? One of them would have to be shifted and scaled to align with the other. I did not see any shift or scaling information in the TIFF file. Tom
On Jul 28, 2016, at 12:55 AM, Marvin Albert wrote:
Hi Elaine,
ok I attached the files here.
I have an image processing pipeline (external to chimera) which segments 3d image stacks and produces a .wrl file (also including meshlab as a tool). I want to use chimera for producing a nice video visualising the individual steps of the segmentation (which consist of .tif and .wrl outputs). If I load in the .wrl and .tif into python for example, coordinates perfectly overlap. Also the coordinates in the raw .wrl file seem to look good.
How does chimera load in the 3d tif stacks?
With kind regards, Marvin
<cube.tif><cube.wrl>
On 27 Jul 2016, at 19:14, Elaine Meng wrote:
Hi Marvin, That link asks for a login, but I can imagine you have two representations of the same object(s) that are not superimposed. (BTW, you can attach images to emails here as long as they aren’t huge.)
…However, I don’t understand where these files came from, and thus why you expect them to be aligned. Did you read a TIFF stack into Chimera as a volume, then contour it, and then export the surface as .wrl? Chimera does not save volumes as .tif, it only saves an image of the graphics window contents in that format, without relationship to the original 3D coordinates.
If some other program wrote the .tif (stack??) and .wrl, I’d put the onus on that program to preserve the coordinate system. Or, maybe it is not possible to preserve 3D coordinates with the .tif format and you’d have to use a real volume format instead of an image stack.
I’m not the expert on this topic, but the others are away. We may need to wait for their opinion(s), but in the meanwhile, clarifying your workflow might help. Thanks, 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 Jul 27, 2016, at 9:49 AM, Marvin Albert wrote:
Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap).
Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh?
(this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3)
Thanks a lot in advance, Marvin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Tom, the cube.tif contains a volume which should align with cube.wrl. However, I just realised the axes x,y,z were inverted as I created the wrl. After fixing this the two volumes overlap perfectly in chimera. Thanks a lot for your help! Marvin
On 2 Aug 2016, at 02:13, Tom Goddard <goddard@sonic.net> wrote:
Hi Marvin,
Your cube.tif file is a stack of 30 images each 50 by 40 pixels. So Chimera displayed it with x, y, and z ranges of 0-50, 0-40, and 0-30. Your VRML file cube.vrml has a cube with x, y, z values ranging from 5-9, 10-14, 15-19. How would you expect these two data sets to align in Chimera? One of them would have to be shifted and scaled to align with the other. I did not see any shift or scaling information in the TIFF file.
Tom
On Jul 28, 2016, at 12:55 AM, Marvin Albert wrote:
Hi Elaine,
ok I attached the files here.
I have an image processing pipeline (external to chimera) which segments 3d image stacks and produces a .wrl file (also including meshlab as a tool). I want to use chimera for producing a nice video visualising the individual steps of the segmentation (which consist of .tif and .wrl outputs). If I load in the .wrl and .tif into python for example, coordinates perfectly overlap. Also the coordinates in the raw .wrl file seem to look good.
How does chimera load in the 3d tif stacks?
With kind regards, Marvin
<cube.tif><cube.wrl>
On 27 Jul 2016, at 19:14, Elaine Meng wrote:
Hi Marvin, That link asks for a login, but I can imagine you have two representations of the same object(s) that are not superimposed. (BTW, you can attach images to emails here as long as they aren’t huge.)
…However, I don’t understand where these files came from, and thus why you expect them to be aligned. Did you read a TIFF stack into Chimera as a volume, then contour it, and then export the surface as .wrl? Chimera does not save volumes as .tif, it only saves an image of the graphics window contents in that format, without relationship to the original 3D coordinates.
If some other program wrote the .tif (stack??) and .wrl, I’d put the onus on that program to preserve the coordinate system. Or, maybe it is not possible to preserve 3D coordinates with the .tif format and you’d have to use a real volume format instead of an image stack.
I’m not the expert on this topic, but the others are away. We may need to wait for their opinion(s), but in the meanwhile, clarifying your workflow might help. Thanks, 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 Jul 27, 2016, at 9:49 AM, Marvin Albert wrote:
Hi all, I process 3d objects and want to visualise them as meshes and volumes simultaneously. However, when I load them into chimera the coordinates of the two are different (meaning they don’t overlap).
Is there an obvious reason for this? Would the volume viewer show a .tif file with different coordinates than chimera shows the .wrl mesh?
(this tiny cube exemplifies my problem: http://www.filedropper.com/cube_3 <http://www.filedropper.com/cube_3>)
Thanks a lot in advance, Marvin
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
participants (3)
-
Elaine Meng -
Marvin Albert -
Tom Goddard