http mipav cit nih gov 1 Medical

http: //mipav. cit. nih. gov 1

Medical Image Processing, Analysis & Visualization in Clinical Research Justin Senseney. J@mail. nih. gov dcb. cit. nih. gov/~senseneyj Biomedical Image Processing Research Services Section Center for Information Technology mipav. cit. nih. gov 2

MIPAV Team Employees Ruida Cheng William Gandler Matthew Mc. Auliffe Evan Mc. Creedy Justin Senseney Fellows Sara Shen (Maryland) Contractors Alexandra Bokinsky, Geometric Tools Inc. (Visualization) Olga Vovk, SRA International Inc. (Technical Writing) Alumni Paul Hemler (Hampden-Sydney), Agatha Monzon, Nishith Pandya (FITBIR), Beth Tyriee (Kentucky), Hailong Wang (Heidelberg) 3

Requirements for an Image Quantification and Visualization Application • Portability – cross-platform or platform-independent execution • Data format independence – access to images: DICOM, Analyze, TIFF, Raw, … • Extensibility – plugins and/or scripts • Scalability – foundation to support the growth to larger and more intricate data structures • Usability – coherent graphical user interface (GUI) 4

Portability Java Primer Source Code Byte Code (class files) Java applications can be "written once and run anywhere", significantly reducing cross -platform development and maintenance. PC Java Interpreter for the PC Machine code UNIX Java Interpreter for a Unix Workstation Machine code 5

Data Independence • • • DICOM file reader/writer DICOM Query/Retrieve and “Catcher” Comprehensive file format support/conversion – http: //mipav. cit. nih. gov/fileformat. html • MIPAV XML file format 6

Extensibility Plugins and Scripts • Plugins – Functions written in Java using the MIPAV API. • Scripts – Use MIPAV to record and save function(s) applied to image dataset(s). – Apply the script to any number of image datasets using the script wizard. 7

Scalability • Model Image is an n-dimensional structure. • Algorithms can support up to 4 D datasets. • Viewers support 4 D dataset with fusion. 8

Usability • GUI elements • Scripting system • Command-line tools 9

10

Functional Overview GUI Views – with data fusion 2 D planar, “Lightbox”, Cine (movie), Multi-planar, 3 D tri-planar, Surface render, (supports 3 D texture mapped volume rendering Volume render VOIs 32 K Manual and automated contouring Algorithms Filtering Segmentation/classification Measurement/quantification Registration/fusion Utilities Plugins S c ri p t i n g Data (Image) types: n-dimensional structure (boolean, byte, unsigned byte, short, unsigned short, int, long, float, double, Complex, ARGB) PACS DICOM 3. 0: Query/Retrieve, Catcher File types (Raw, Analyze, DICOM 3. 0, GE, Siemens, Bruker, Interfile, Micro cat, MINC, MRC, FITS, Cheshire, AFNI, TIFF, JPEG, GIF, BMP, AVI, Quick. Time, Biorad, Ziess LSM 510, XML, and more) 11

Opening Images 12

Opening Images 13

Image Browser 14

Opening Images 15

Saving Image As (use suffix) 16

Code Snapshot int dest. Extents[] = new int[2]; dest. Extents[0] = image. get. Extents()[0]; dest. Extents[1] = image. get. Extents()[1]; // X dim // Y dim // Make a result image of Unsigned byte type result. Image = new Model. Image(Model. Storage. Base. UBYTE, dest. Extents, “Result Image”, null); int length = dest. Extents[0] * dest. Extents[1]; for (int i = 0; i < length; i++){ dest. Image. set(i, i%256); } View. JFrame. Image image. Frame; Model. LUTa = new Model. LUT(Model. LUT. COOLHOT, 256, dim. Extents. LUT); image. Frame = new View. JFrame. Image(result. Image, LUTa, new Dimension(610, 200), user. Interface); 17

Algorithms • Filters • Calculation • Registration • Transformation • Surface extraction • Classification/Segmentation 18

Download and Setup 1. http: //mipav. cit. nih. gov/download 2. Fill in form 3. Install (e. g. install. MIPAV. exe) ** Nightly download - lastest changes but might have bugs. ** Archived releases also available. 19

Memory Allocation General Rules • Do not exceed the computer’s physical RAM. For example if the computer has 1 GB do not exceed approx 800 MB. • For 32 -bit Windows systems do not exceed 1, 400 MB 20

Memory Usage Press to recover memory 21

MIPAV Program Options 22

Digital Image Communication in Medicine (DICOM). American College of Radiology (ACR) and the National Electrical Manufacturers Association (NEMA) formed a joint committee in 1983 to develop a standard in Digital Image Communication in Medicine (DICOM). 1. Promote communication of digital image information, regardless of device manufacturer 2. Facilitate the development and expansion of picture archiving and communication systems (PACS) that can also interface with other systems of hospital information 3. Allow the creation of diagnostic information databases that can be interrogated by a wide variety of devices distributed geographically. 23

DICOM Model Internet PACS 24

DICOM communication interface 25

DICOM 26

DICOM Access to image header information 27

DICOM Anonymization 28

DICOM File Browser 29

XML Schema File Format 30

XML Schema File Format 31

XML Schema File Format 32

Image Attributes 33

Volume of Interest (VOI) 34

VOI 35

Lookup Table (LUT) 36

Multi-planar and Lightbox 37

Image Fusion The loading of two images into the same frame Controls blending between the two images 38

Structural MRI and Functional MRI 39

Animation Tool 40

Masks and Surfaces 41

Scripting - Record 42

Scripting - Run 43

Help 44

Bug Report 45

MIPAV Visualization Macros/Plugins Processing Quantification Ubiquitous file reader File writer 46

http: //mipav. cit. nih. gov Senseney. J@mail. nih. gov 47