Hi,
I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this?
Thank you,
-- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France
Hi Christophe, We’re glad you like the blob-measurement tool!
The input volume data (3D image, density map, etc.) and the chosen contour level define the blobs, i.e. disconnected parts of a contour surface. The contour level setting should be saved in a session, and the volume data can either be kept separately in its original file, which is the default since the data file might be very large, or included in the session file (using “save” command option “includeMaps true”). http://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#session
The “Measure and Color Blobs” tool simply recolors and reports sizes of individual clicked blobs; it does not do a segmentation calculation (other than to identify completely disconnected parts) or create new objects. http://rbvi.ucsf.edu/chimerax/docs/user/tools/measureblobs.html
If you mean you want to keep the record of what exactly was clicked and the resulting size, that should all be in the Log, which you can save with “Save As…” in the context menu of the Log, or command “log save” http://rbvi.ucsf.edu/chimerax/docs/user/tools/log.html http://rbvi.ucsf.edu/chimerax/docs/user/commands/log.html
I tried saving a session after measuring blobs, and I see that restoring loses the coloring. Did you mean you wanted to retain the coloring? That may be a current limitation.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 27, 2019, at 2:41 AM, Christophe Leterrier christophe.leterrier@gmail.com wrote:
Hi, I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this? Thank you, -- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France
Hi Christophe,
I fixed ChimeraX session save so that it will preserve the coloring of the blobs in session files. That will be in tonight's Chimerax builds. If you change the image threshold it loses the coloring.
What kind of independent object for the picked blob do you want? What quantification are you planning to do on it? Does it need to be an extracted subvolume? Would the subvolume be axis-aligned, or rotated, and with how much padding? Would it be masked so all values outside the picked blob are 0? That creates rather horrible edges unless the mask rolls off gradually -- but roll off requires parameters and an algorithm. Or do you just want the surface of the the blob copied?
For picking all blobs, usually there is too much noise for that to be useful. Maybe you would want some size cutoff. Or maybe you would have to cull by hand -- that culling would require some new mouse mode.
ChimeraX is primarily for interactive exploration of data, not automated processing. Your requests could be useful features but it would need a clear use case with the details explained so we could decide whether it is useful to many people (in which case we might implement it) or is too specialized for general use.
Tom
On Nov 27, 2019, at 2:41 AM, Christophe Leterrier christophe.leterrier@gmail.com wrote:
Hi,
I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this?
Thank you,
-- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Tom,
Found this old thread, and wanted to pick up on it.
I used the mouse right-click mode to select and color a blob (and measure it). What I would like to do is display the surface of this blob without displaying the rest of the map. This way, I could make a figure with, say, my atomic model, plus this unidentified blob next to it. The way I've done this in the past is to build some model inside the blob and then do "volume zone" near those atoms, but I'd rather not have to do that if possible - it takes a while.
I'd love a way to create a surface object from the select blob, so that I could show that object and hide the original map.
Is this possible?
Cheers, Alexis
On Wed, Nov 27, 2019 at 11:10 AM Tom Goddard goddard@sonic.net wrote:
Hi Christophe,
I fixed ChimeraX session save so that it will preserve the coloring of the blobs in session files. That will be in tonight's Chimerax builds. If you change the image threshold it loses the coloring.
What kind of independent object for the picked blob do you want? What quantification are you planning to do on it? Does it need to be an extracted subvolume? Would the subvolume be axis-aligned, or rotated, and with how much padding? Would it be masked so all values outside the picked blob are 0? That creates rather horrible edges unless the mask rolls off gradually -- but roll off requires parameters and an algorithm. Or do you just want the surface of the the blob copied?
For picking all blobs, usually there is too much noise for that to be useful. Maybe you would want some size cutoff. Or maybe you would have to cull by hand -- that culling would require some new mouse mode.
ChimeraX is primarily for interactive exploration of data, not automated processing. Your requests could be useful features but it would need a clear use case with the details explained so we could decide whether it is useful to many people (in which case we might implement it) or is too specialized for general use.
TomOn Nov 27, 2019, at 2:41 AM, Christophe Leterrier <
christophe.leterrier@gmail.com> wrote:
Hi,
I started using ChimeraX for visualization and quantification of 3D
microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this?
Thank you,
-- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Hi Alexis,
This feature was requested about a year ago and there is a ticket for it
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2103 https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2103
It has not been worked on and there is no easy way to do it in ChimeraX right now. Maybe a checkbutton option that makes a separate blob model each time one is picked could be added ("copy blobs"). There are 288 open feature requests now and 232 bugs for ChimeraX, probably about 2 years of work by current staff to catch up if we had nothing else to do, we can't get to everything. This is one of those things that so far has been of too narrow a use to get attention.
Tom
On May 11, 2020, at 4:54 PM, Alexis Rohou a.rohou@gmail.com wrote:
Hi Tom,
Found this old thread, and wanted to pick up on it.
I used the mouse right-click mode to select and color a blob (and measure it). What I would like to do is display the surface of this blob without displaying the rest of the map. This way, I could make a figure with, say, my atomic model, plus this unidentified blob next to it. The way I've done this in the past is to build some model inside the blob and then do "volume zone" near those atoms, but I'd rather not have to do that if possible - it takes a while.
I'd love a way to create a surface object from the select blob, so that I could show that object and hide the original map.
Is this possible?
Cheers, Alexis
On Wed, Nov 27, 2019 at 11:10 AM Tom Goddard <goddard@sonic.net mailto:goddard@sonic.net> wrote: Hi Christophe,
I fixed ChimeraX session save so that it will preserve the coloring of the blobs in session files. That will be in tonight's Chimerax builds. If you change the image threshold it loses the coloring.
What kind of independent object for the picked blob do you want? What quantification are you planning to do on it? Does it need to be an extracted subvolume? Would the subvolume be axis-aligned, or rotated, and with how much padding? Would it be masked so all values outside the picked blob are 0? That creates rather horrible edges unless the mask rolls off gradually -- but roll off requires parameters and an algorithm. Or do you just want the surface of the the blob copied?
For picking all blobs, usually there is too much noise for that to be useful. Maybe you would want some size cutoff. Or maybe you would have to cull by hand -- that culling would require some new mouse mode.
ChimeraX is primarily for interactive exploration of data, not automated processing. Your requests could be useful features but it would need a clear use case with the details explained so we could decide whether it is useful to many people (in which case we might implement it) or is too specialized for general use.
TomOn Nov 27, 2019, at 2:41 AM, Christophe Leterrier <christophe.leterrier@gmail.com mailto:christophe.leterrier@gmail.com> wrote:
Hi,
I started using ChimeraX for visualization and quantification of 3D microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this?
Thank you,
-- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France _______________________________________________ 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
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
Thanks Tom,
Fair enough. I ended up doing it with the volume eraser - not too bad, especially thanks to the "erase outside of sphere" option.
Cheers, Alexis
On Mon, May 11, 2020 at 5:18 PM Tom Goddard goddard@sonic.net wrote:
Hi Alexis,
This feature was requested about a year ago and there is a ticket for it
https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/2103
It has not been worked on and there is no easy way to do it in ChimeraX right now. Maybe a checkbutton option that makes a separate blob model each time one is picked could be added ("copy blobs"). There are 288 open feature requests now and 232 bugs for ChimeraX, probably about 2 years of work by current staff to catch up if we had nothing else to do, we can't get to everything. This is one of those things that so far has been of too narrow a use to get attention.
Tom
On May 11, 2020, at 4:54 PM, Alexis Rohou a.rohou@gmail.com wrote:
Hi Tom,
Found this old thread, and wanted to pick up on it.
I used the mouse right-click mode to select and color a blob (and measure it). What I would like to do is display the surface of this blob without displaying the rest of the map. This way, I could make a figure with, say, my atomic model, plus this unidentified blob next to it. The way I've done this in the past is to build some model inside the blob and then do "volume zone" near those atoms, but I'd rather not have to do that if possible - it takes a while.
I'd love a way to create a surface object from the select blob, so that I could show that object and hide the original map.
Is this possible?
Cheers, Alexis
On Wed, Nov 27, 2019 at 11:10 AM Tom Goddard goddard@sonic.net wrote:
Hi Christophe,
I fixed ChimeraX session save so that it will preserve the coloring of the blobs in session files. That will be in tonight's Chimerax builds. If you change the image threshold it loses the coloring.
What kind of independent object for the picked blob do you want? What quantification are you planning to do on it? Does it need to be an extracted subvolume? Would the subvolume be axis-aligned, or rotated, and with how much padding? Would it be masked so all values outside the picked blob are 0? That creates rather horrible edges unless the mask rolls off gradually -- but roll off requires parameters and an algorithm. Or do you just want the surface of the the blob copied?
For picking all blobs, usually there is too much noise for that to be useful. Maybe you would want some size cutoff. Or maybe you would have to cull by hand -- that culling would require some new mouse mode.
ChimeraX is primarily for interactive exploration of data, not automated processing. Your requests could be useful features but it would need a clear use case with the details explained so we could decide whether it is useful to many people (in which case we might implement it) or is too specialized for general use.
TomOn Nov 27, 2019, at 2:41 AM, Christophe Leterrier <
christophe.leterrier@gmail.com> wrote:
Hi,
I started using ChimeraX for visualization and quantification of 3D
microscopy images. The "blob" tool is particularly impressive to semi-automatically segment objects of interest and measure their characteristics. However, I could not find a way to generate an independent object from the picked blobs. This makes the quantification process unreproducible as it is not possible to store the blobs in the session or automatically measure all the picked blobs. Am I wrong in the intent of the tool, or is there a way to do this?
Thank you,
-- Christophe Leterrier NeuroCyto lab INP CNRS UMR 7051 Aix Marseille University, France _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (4)
-
Alexis Rohou -
Christophe Leterrier -
Elaine Meng -
Tom Goddard