Hi Dominic, Ok, here is a way to do what you described that does not need any Python. First you place a marker at the enter of the green blob using ChimeraX Markers toolbar using the Center mode (mark center of connected surface). Once you select that mouse mode, right click on the green blob to place the marker. Then make a sphere centered at that marker with the shape command, e.g. "shape sphere center #3 radius 100". Then mask the red map to get just the part inside that sphere, e.g. "volume mask #1 surface #4". Then measure the volume enclosed in that masked map surface, e.g. "measure volume #5". You might also be interested in exactly how much red blob is inside the green blob and you could mask the red using the surface of the green to do that. Tom

On Oct 8, 2021, at 2:33 AM, BINGHAM Dominic <dominic.BINGHAM@univ-amu.fr> wrote:

The custom python code sounds more applicable to what I am doing. I will give that a try but also would greatly appreciate some tips

To give context, I have several maps like shown above, with 2-channels showing the staining of one protein each. Each map is a synapse, and these are taken from 3D-STORM images contains several synapses. I have 3 different conditions, and I would like to compare what I measure and how it changes between these conditions. So for instance, ideally, what I would like to do is to measure from the centre of the large green structure which is colocalised to the large red structure (Circle on image above). I would then like a value to represent the relative amount of the ‘red’ protein within a set volume around the ‘green’ structure. I would then compare this value between each condition.

So any tips on the code for python would be great here!

Thanks so much for the help!

Dominic

...

Le 6 oct. 2021 à 20:08, Tom Goddard <goddard@sonic.net <mailto:goddard@sonic.net>> a écrit :

Hi Dominic,

The ChimeraX Distances tools measures distances between atoms in an atomic structure. You have image data, not an atomic structure so that is why it will not report any distances.

One way to proceed would be to place a marker on every connected surface piece in each of the two images, then measure distances between these centroid markers. There is code to place the markers using ChimeraX here

https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html <https://rbvi.github.io/chimerax-recipes/mark_blobs/mark_blobs.html>

Markers are treated just like atoms in ChimeraX so the Distance tool would work. But you want all nearby distances so you might try the Contacts tool

https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/clashes.html>

That may not give you what you want. Very likely you would need to write some custom Python code to get exactly what you want. Probably you also want the volume enclosed in each blob. If you need tips on how to write that Python code I can advise if you give specifics of what you want.

Tom

...

On Oct 6, 2021, at 4:11 AM, BINGHAM Dominic via ChimeraX-users <chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@cgl.ucsf.edu>> wrote:

Hello,

I have a problem with which I’m trying to use chimeraX to solve. I have some images of synapses with which I have super-resolved two proteins in 3D (so two images/channels). I want to quantify the colocalisation of a structure of one protein to the blobs of the other protein within a certain distance. Shown below is the non-segmented map of the 2 images of proteins. So for example I would want to quantify the colocalisation of the red blobs within a certain distance of specific larger green blobs. I want to then compare these between different conditions. <Capture d’écran 2021-10-06 à 12.58.42.png>

I have segmented the images already using "segmentat map ». I have been trying to start with the « distance » tool to measure how far one blob of protein is from the structure (Image shown below of two selected structures in just the map of one protein to practice).

<Capture d’écran 2021-10-06 à 12.57.28.png>

However, this doesn’t seem to work functionally as no distance is shown when I try to perform the function. Also, this function may possibly be too basic for what Im trying to do. That said, any help on how to use this function would still be greatly appreciated.

Ultimately, I think the best thing for what I would like is to be able to select a specific structure and have a measurement of all the blobs of the other protein within a defined 3D radius of this structure, and then compare this value between different conditions. I have been looking through the user manual and I can’t seem to find anything that will do something like this… I (and my PhD) would be monumentally grateful if you could possibly help me with this problem? Either by pointing me to the correct function, or even a thread that has discussed a similar problem that I may have missed?

Thanks and have a wonderful day,

Dominic Bingham PhD student at Aix-Marseille University

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