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

[Alexis Rohou]

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 at 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 at 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 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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