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

[Elaine Meng]

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 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