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h2. {color:blue}{*}X-Ray Reconstruction of Moving Morphology (XROMM) is an x-ray imaging and computational process that produces precise and accurate 3D movies of skeletal movement.*{color} 

h4. See [|] for more information.{center}
h4. \* [Recent Changes and Downloads|Recent Changes]

h2. {color:blue}There are seven steps in the marker-based XROMM workflow:{color}

h3. 1) Implant radiopaque bone markers

h3. 2) Record biplanar x-ray videos of movement

* For Brown Users: [Getting trained and certified to use x-ray machines|Getting certified to use x-ray equipment] and [Operating C-arm x-ray machines during data collection|C-arm fluoroscope operating instructions]
* We recommend reading [Radiographics papers|] for background on x-ray imaging

h3. 3) Analyze x-ray videos to extract XYZ coordinates of radiopaque markers

* [Digitizing x-ray movies using the MATLAB XrayProject.mat procedure|MATLAB XrayProject digitizing instructions]. (MATLAB scripts written by Ty Hedrick and Dave Baier, and modified and updated by Loretta Reiss)

h3. 4) Create 3D  polygonal bone surface models

* [Creating 3D models from CT scans using Amira software|Creating 3D CT models using Amira software]
* [Creating 3D models with Microscan Laser Scanner|Laser Scanning Protocol]
* [Creating 3D models with OsiriX]

h3. 5) Measure XYZ coordinates of markers relative to polygonal bone models

* [Instructions|Create a Setup Scene in Maya] for this step are available if you are working with models from CT scans. Laser scan procedures are different and instructions are not yet available.
* For CT models, this step is done in Maya using the [XROMM Maya Tools|Download and Install Maya MEL scripts]

h3. 6) Calculate rigid body kinematics from XYZ marker positions

* [Calculate Rigid Body Motion in Matlab]

h3. 7) Produce XROMM animations in Autodesk Maya

* [Maya Magic: Creating and analyzing XROMM animations using MATLAB and Autodesk Maya|Importing models into Maya and working with models]

h2. {color:blue}For markerless XROMM,{color} {color:blue}[create Maya x-ray cameras and load undistorted video into Maya|Recreate Xray cameras in Maya]{color}{color:blue}, then create{color} {color:blue}[rotoscoping controls|Rotoscope Set-up]{color}

h4. \* Note: If you want to remove fluoroscope distortion from x-ray movies (i.e. undistort or correct the movies), use [X-rayProject version 2 or later|X-Ray Reconstruction of Moving Morphology (XROMM)^]. We are no longer updating VideoCorrect or FluoroCorrect MATLAB programs. Undistorting a video is a two-step process: 1. [Create an \*UNDTFORM file|Creating an *UNDTFORM file] and 2. Click *Undistort Video* in the [X-rayProject window|MATLAB XrayProject digitizing instructions].


CRITICAL UPDATE: Use new XMALab software for marker-based XROMM, and also for undistorting and calibrating biplanar X-ray setups.

XMALab replaces MATLAB XrayProject. See Bitbucket XMALab wiki for XMALab User Manual (not this wiki). 

Note: there is a Table of Contents we recommend you use to navigate this xrommwiki. The links on this page are obsolete.


X-Ray Reconstruction of Moving Morphology (XROMM) is an X-ray imaging and computational process that produces precise and accurate 3D movies of skeletal movement.

z_*OBSOLETE* Recent Changes and DOWNLOADS
Brown XROMM Short Courses


At Brown University we have developed three main approaches to XROMM:

1) Marker-based XROMM workflow (Brainerd et al., 2010)
2) Scientific Rotoscoping workflowi.e. manual markerless XROMM (Gatesy et al., 2010)
3) XROMM AutoScoper software, i.e. automated markerless XROMM (Miranda et al., 2011)
New: XROMM Undistorter, stand-alone undistortion program

We have also developed the X-ray Motion Analysis Portal (XMA Portal) for storing, viewing and managing X-ray movie data and associated metadata.

Resources for Keck Foundation XROMM Core Facility

This wiki contains instructions and software downloads, contributed by many users. See and the publications below for general information about XROMM. 

Brainerd, E.L., D.B. Baier, S.M. Gatesy, T.L. Hedrick, K.A. Metzger, S.L. Gilbert, and J.J. Crisco. (2010) X-ray Reconstruction of Moving Morphology (XROMM): precision, accuracy and applications in comparative biomechanics research. Journal of Experimental Zoology, 313A: 262-279.

Gatesy S.M., Baier D.B., Jenkins F.A., Dial K.P. (2010) Scientific rotoscoping: a morphology-based method of 3-D motion analysis and visualization. Journal of Experimental Zoology, 313A:244--261.

Miranda, D.L., Schwartz, J.B., Loomis, A.C., Brainerd, E.L., Fleming, B.C., Crisco, J.J. (2011) Static and Dynamic Error of a Biplanar Videoradiography System Using Marker-Based and Markerless Tracking Techniques. Journal of Biomechanical Engineering, 133 (12): 1-8.

Knörlein, B.J., Baier, D.B., Gatesy, S.M., Laurence-Chasen, J.D. and Brainerd, E.L. 2016. Validation of XMALab software for marker-based XROMM. Journal of Experimental Biology, 219: 3701-3711. doi: 10.1242/jeb.145383.