id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
449	Volume planes on multiple data display is erratic	meng@…	Tom Goddard	"Looks like volume planes command to cycle through planes when applied to multiple datasets that are different optical microscopy channels may not correctly handle the blending.

Begin forwarded message:

From: Elaine Meng <>
Subject: Re: Graham data, reasonable ChimeraX session
Date: October 13, 2016 at 11:04:35 AM PDT
To: Tom Goddard 


Hi Tom,
Graham-data script take 2...

Script attached, setup2.cxc. Changes from the first one, setup.cxc, are that I set each of the 4 imaging datasets to step 1 and made the top levels to go to the max value, and used the volume command instead of “transparency” to make the 4 segmentation meshes transparent.

I noticed that the data looks very “sandwich-y” in that the middle Z layers have much less intensity than the perimeter of the cell, and if you rotate 90 degrees you can barely see anything.  I thought it might be a rendering weirdness in ChimeraX, but it seems to be the same way in Chimerax.  

I also attach another Chimera session with colors and levels the same as in the ChimeraX script setup2.cxc and a side-by-side image comparison, so that you can see the blending difference.  (The model numbers aren’t the same in the session vs. the script, though… sorry).  As you’re probably well aware, there are more white spots in ChimeraX where data peaks overlap.

A possible bug (prioritize as desired): I was running volume planes to try to understand whether there was really data in the middle of the sandwich or not, and discovered that if I run this command repeatedly in ChimeraX (after setup2.cxc) I get different playbacks, sometimes only containing one of the datasets, and after about 10x, sometimes none of the datasets. 

volume #1,3,5 planes z,1,1000,1,10

In the Chimera session, the corresponding command does give a consistent result upon repeated use:

volume #1,2,4 planes z,1,1000,1,10

Elaine"	defect	closed	major		Volume Data		wontfix						all	ChimeraX