id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
6255	Make DICOM reader read time series from 2D images	goddard@…	Zach Pearson	"Jason Rubenstein asked about displaying a DICOM time series consisting of 1000 2D images which represent 25 times, each a 3D image of 40 planes.  He provided example data (series0079-Body.zip) to Elaine.  It opens in ChimeraX 1.3 with menu File / Open DICOM Folder as if it is a single 3D image of 1000 planes.  But by splitting the .dcm files into 25 subdirectories ChimeraX can open as 25 3D images and play through them with the mseries command.  I've attached a Python scripted I used to put the planes in subdirectories.

Another issue was that the ChimeraX DICOM reader assigned a bad rotation to each volume that goofed up the orthoplanes view -- making the 3 planes not align with the displayed data.  To visualize orthoplanes I set the rotation to no rotation with a Python script (attached).

I am not attaching the data as it may be confidential.  Here is his original ChimeraX mailing list question

https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2022-February/003386.html"	enhancement	closed	moderate		DICOM		fixed		Elaine Meng			jrubenstein@mcw.edu	all	ChimeraX