[chimerax-users] Map "Blobs" tool - Generate objects?

[Alexis Rohou]

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 at 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.
>
>         Tom
>
>
> > On Nov 27, 2019, at 2:41 AM, Christophe Leterrier <
> christophe.leterrier at 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
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