6. Weekly Meetings
The University of Texas at Austin
Austin, Texas 78712
- July. 1, 2008: Optical Flow
- Apr. 17, 2008: Review of In-Vivo Canine Experiment
- Apr. 3, 2008: Amira, Cubit, AVS, and Control
- Mar. 6, 2008: In-Vivo Experiments
- Jan 15, 2008: Project Overview
- December 5, 2007: Project Update
- Sept 20, 2007: Presentation of Adv. Num. HT paper
- Sept 6, 2007: Molecular Imaging
- Aug 30, 2007: Cell Viability
- Aug 9, 2007: Project Update
- July 5, 2007: Project Update
- May 31, 2007: Project Update
- April 30, 2007: Project Overview
- Apr 26, 2007: Laser Source Term Part II
- April 19, 2007: Cell Damage Modeling
- April 19, 2007: Cell Viability Part II
- April 12, 2007: Cell Viability Part I
- March 29, 2007: Project Update
- March 1, 2007: Laser Source Term
- February 22, 2007: Image Registration
- February 15, 2007: Registration
- February 8, 2007: Calibration
- Feb 1, 2007: Outline of MRI phantom experiments to test serial image registration algorithms.
- Jan 22, 2007: Image/Geometry Registration
- January 8, 2007: R01 Proposal
- Oct 30, 2006: Cell Damage Modeling
- August 24, 2006: The Control Loop
- June 22,2006: Dynamic Control Loop/MAFLEP
- June 8,2006: The Control Loop
- May 25, 2006: The Control Loop: Inverse Problem and Calibration
- April 27, 2006: Solution Technique of Adjoint Problem
- April 20, 2006: Plan on Cellular Experiments
- April 13, 2006: Perfusion Effect of Vasculature Structures in BioHeat Transfer
- Feb. 23, 2006: Application of MRI and MRTI in Cancer Treatment
- Feb.9 and Feb. 16, 2006: Visualization Software Suite and Finite Element Meshing From Imaging Data
- Jan. 2006: DDDAS Workshop Presentation
- Jan. 26, 2006: Computational Infrastructure for DDDAS Project
- Dec. 2005: Introduction to Cellular Biology
- Nov. 2005: Special Topics in Biology
- Nov. 2005: Design of Optimal Laser Protocols for Prostate Cancer by Controlling Heat Shock Protein Expression
July. 1, 2008: Optical Flow
Apr. 17, 2008: Review of In-Vivo Canine Experiment
Apr. 3, 2008: Amira, Cubit, AVS, and Control
Mar. 6, 2008: In-Vivo Experiments
Jan 15, 2008: Project Overview
December 5, 2007: Project Update
Sept 20, 2007: Presentation of Adv. Num. HT paper
Sept 6, 2007: Molecular Imaging
Alfred Song made a presentation on Molecular Imaging [ppt]
Aug 30, 2007: Cell Viability
Sepideh Koshnevis, Cell Viability [ppt]
Aug 9, 2007: Project Update
David Fuentes, Project Update [pdf]
July 5, 2007: Project Update
David Fuentes, Project Update [pdf]
May 31, 2007: Project Update
David Fuentes, Project Update (May 31, 2007) [pdf]
April 30, 2007: Project Overview
Apr 26, 2007: Laser Source Term Part II
Andrea Hawkins, Laser Source Term Part II [pdf]
April 19, 2007: Cell Damage Modeling
Yusheng Feng, Cell Damage Modeling (April 19, 2007) [ppt]
April 19, 2007: Cell Viability Part II
Sepideh Koshnevis, Cell Viability Part II (April 19, 2007) [ppt]
March 29, 2007: Project Update
David Fuentes, Project Update [pdf]
March 1, 2007: Laser Source Term
Andrea Hawkins first discussed how the energy from the laser is completely converted into heating since the light does no work on the system [pdf]. Various optical properties and definitions and their relevance to our source term were also discussed. Finally, a theorem was introduced which stated certain assumptions and gave a result of an appropriate source term which is close to our current source term. The proof of this will be presented later.
February 22, 2007: Image Registration
Aman Rathi presented his progress on Image Registration Problem for the project [ppt] As we know that we would be getting a prostate image days before the actual operation day. Hence, the mesh computations etc would have already been carried out on that preliminary image. On the actual operation day, we will again get images from MDA of the same prostate but they may be shifted, rotated etc due to contingent factors. To do any meaningful computations on this new image and to make sense of the computations on the previous image, we need to register this new image to the previous image. And hence, we require Image Registration of 3D images. The Image registration is of two types : Feature based and Area based. Feature based registration requires use of landmarks or features which unfortunately are hard to find in biological tissue images. Hence, we would go for Area based registration which uses FFT and other structural features of the image to co-register them. Then, we outlined the Image registration algorithm as stated in the paper . The algorithm finds out the shift. rotation and the scale difference between the two images. We also set up a small experiment on the AVS to show that the code works well for two 2D-images. Future work includes rigorous testing of the 2D code and converting it to 3D.
1. R. Araiza et al. 3-D Image Registration Using Fast Fourier Transformation: Potential Applications to Geoinformatics and Bioinformatics.
February 15, 2007: Registration
A list of priorities concerning meshing, visualization, and computational capabilities for the May 2007 Conference in Beijing was discussed. [pdf] The goal for the conference is to present an end-to-end solution: preoperative data acquisition, mesh generation, optimal laser control, intraoperative data acquisition, mesh registration, calibration, visualization, and feedback.
- Mesh registration is the highest priority. The current plan is to attack mesh registration in two steps.
- Use FFT to eliminate rigid body motions between two sets of 3d images. Current progress on this will be presented at the meeting on February 22, 2007.
- Once rigid body motion has been eliminated, relatively small deformations of the mesh can be used for registration of intraoperative images.
Also needed is to agree upon a mesh file format in which meshes generated by LBIE can be viewed seamlessly in Volrover.
- The Volrover server must be updated so that it is intranet aware with the computational server on Lonestar. i.e. David and Bongjune must communicate to discuss how to connect Hp3d with Volrover via XML-RPC. Also, the machine to run the Volrover visualization server must be decided upon.
- Hp3d must be made internet aware of the data server in Houston to transfer the MRTI thermal images. Choosing a suitable objective function for the calibration problem is still work in progress.
February 8, 2007: Calibration
David Fuentes presented latest computational results [pdf]. The objective function for the calibration problems needs to be modifying as the parameters be found are out of the acceptable bounds.
Feb 1, 2007: Outline of MRI phantom experiments to test serial image registration algorithms.
Dr. Diller gave a summary of the MRI experiments designed to acquire MRI imaging data to test the image registration code [doc] . The data will be posted off of the website when it is available. David Fuentes presented the python script used for automatic data transfer [pdf]. The current script scp’s the data to the remote machine. Dr. Bajaj suggested a looking into XML-RPC to transfer the data to avoid writing to disk.
Jan 22, 2007: Image/Geometry Registration
Chandrajit Bajaj, Image/Geometry Registration [pdf]
Dr. Bajaj presented his in house image registration software today. Two topics were presented: fusion and geometry registration. Fusion is not needed as the same machine acquires both the MRTI and MRI data. The primary concern for the meeting is the geometry registration problem. The following two-step plan was proposed to solve the geometry registration problem:
- Align rigid body motions assuming no mesh deformation.
- Once rigid body motion has been eliminated, update the mesh assuming small deformations.
The current action item is to test the available software to perform rigid body image registration.
January 8, 2007: R01 Proposal
The NIH R01 proposal was discussed. Dr. Diller, Dr. Hazle, and Dr. Stafford have been conversing over adding cell permeability as an indicator of cell viability to the next proposal. The January 24th deadline for the NIH proposal is unfeasible. The DDDAS teams agrees on applying to the May Deadline for the NIH R01 grant. Dr. Diller will send literature on the relationship between cell permeability and cell viability/cell stess/cell damage to Andrea and she will broadcast it to the group.
The remaining task for completing the control loop is to align the mesh that Jessica creates prior to treatment to the biological domain the day of treatment. This is an image registration problem and several methods are available as a solution including:
- Dr. Bajaj has an in-house code setup for image registration. It is currently setup for 2D image registration and capable of registering translations, rotations.
- This website [link] claims that they have a code to perform the image registration.
- A simple code can be written using existing data structures that will do an image registration ASSUMING ONLY rigid body rotation and translation.
However, the first order of business is to obtain a data set from MDA from which we can test the image registration code.
February is the next scheduled laser treatment of a canine at MDA. Testing of every aspect (automatic data transfer, filtering, computations, visualization) of the DDDAS code is scheduled for the month of January. The code must be tested on a simulated control loop environment and must demonstrate reliability during both the simulated laser treatment as well as phantoms runs on agar and ex vivo tissue before being considered for use on a living subject.
Oct 30, 2006: Cell Damage Modeling
Yusheng Feng, Cell Damage Modeling [pdf]
August 24, 2006: The Control Loop
David Fuentes, The Control Loop [pdf] movies: original mri data [mpg] finite element mesh [mpg] fem prediction vs MRTI [mpg]
On Aug 17, Dr. Yusheng Feng gave a report on Joint SIAM-SMB Conference on Life Sciences, which he attended at the beginning of August.
There will be a video-conference with M.D. Anderson this Thursday (Aug. 24, 2006) in ACES Room 6.336 at 2:00PM.
June 22,2006: Dynamic Control Loop/MAFLEP
Dr. Yusheng Feng presented “Dynamic Control Loop: An Overview.” [ppt]
David Fuentes presented “Dynamic Control Loop: Implementation Strategy.” [pdf]
Dr. Oden gave a presentation at the MAFLEP conference [pdf]
June 8,2006: The Control Loop
David Fuentes presented “The Control Loop: Optimal Control of Laser.” [pdf]
May 25, 2006: The Control Loop: Inverse Problem and Calibration
David Fuentes, The Control Loop: Inverse Problem and Calibration [pdf]
David Fuentes presented “The Control Loop: Inverse Problem and Calibration” – a status report (May 25, 2006).
Prof. Ken Diller presents “A Dynamic Data-Driven System for Laser Treatment of Cancer” in International Conference on Computational Science, Reading, U.K. (May 28-31, 2006). [pdf]
David Fuentes, Dissertation proposal. [pdf]
April 27, 2006: Solution Technique of Adjoint Problem
David Fuentes, Solution Technique of Adjoint Problem [pdf]
David Fuentes presented “Solution Technique of Adjoint Problem” – a status report (April 27, 2006).
April 20, 2006: Plan on Cellular Experiments
Sepideh Koshnevis presented her plan on cellular experiments [ppt]
April 13, 2006: Perfusion Effect of Vasculature Structures in BioHeat Transfer
Yusheng Feng presented “Perfusion Effect of Vasculature Structures in BioHeat Transfer” – a new formulation for bioheat transfer with vascular effect (April 13, 2006).
Feb. 23, 2006: Application of MRI and MRTI in Cancer Treatment
John Hazle, Application of MRI and MRTI in Cancer Treatment Dr. Hazle from M.D. Anderson will visit Austin to join the project meeting this week (02/23/06) and give a talk on the MRI and MRTI technologies.
Feb. 9 and Feb. 16, 2006: Visualization Software Suite and Finite Element Meshing From Imaging Data
S. Goswami and Jessica Zhang, Visualization Software Suite and Finite Element Meshing From Imaging Data [pdf]
S. Goswami and Jessica Zhang presented preliminary results for visualization and capability of their software suite on 02/09/06 and 02/16/06.
Jan. 2006: DDDAS Workshop Presentation
Leszek Demkowicz, DDDAS Workshop Presentation (Jan. 2006) at Washington D.C. [pdf]
Dr. Demkowicz represented our team and gave a presentation at DDDAS workshop held Jan. 19-20, 2006 at D.C. while Dr. Prudhomme was the other member of the delegation.
Jan. 26, 2006: Computational Infrastructure for DDDAS Project
David presented a strategy of model calibration and dynamic control using MRTI feedback data. [pdf]
Dr. Jason Stafford and two of his associates from M.D. Anderson visited Austin and attended the project meeting.
Dec. 2005: Introduction to Cellular Biology
David Fuentes, Introduction to Cellular Biology [pdf]
Nov. 2005: Special Topics in Biology
Nichole Rylander, Special Topics in Biology [pdf]
Nov. 2005: Design of Optimal Laser Protocols for Prostate Cancer by Controlling Heat Shock Protein Expression
Dr. Nichole Rylander gave presentations on her dissertation research and biological aspect of DDDAS project.
Nichole Rylander, Design of Optimal Laser Protocols for Prostate Cancer by Controlling Heat Shock Protein Expression [pdf] [pdf] Prof. Diller led part of the Austin team visited M.D.Anderon Cancer Center and met with Prof. Hazle and his Houston team on December 7, 2005.