interoperability of imaging data file formats: the mpscope case quoc-thang nguyen physics...
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Interoperability of Imaging Data File Formats:The MPScope Case
Quoc-Thang NGUYEN
Physics Department, UCSD
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Multiphoton laser fluorescence scanning microscopy.
• Multiphoton Laser Fluorescence Scanning Microscope (MPLFSM):
Focus high energy, femtosecond laser pulse to excite fluorescent dye:
2 photons @ 800 nm ~ 1 photon @ 400 nm
• MPLFSM versus other Fluorescence Microscopes:
No out of focus z-sectioning, sharp contrast excitation
Longer Better penetration in scattering tissue
Smaller excitation Less dye bleaching volume Better resolution
More photons collected
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Brightfield vs. Multiphoton
Trigeminal Ganglion Neurons loaded with Calcium Green
Zeiss Axioplan 2Microscope
Cooled CCD CameraFuzzy images, severe bleaching
Multiphoton LaserScanning Fluorescence
Microscopez-sectioning
500
m40 xWater
ImmersionObjective
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Custom-built multiphoton microscopes
Used in Neuroscience, Immunology, Developmental Biology...
Commercial two-photon scopes: $750K
Custom-made 2P scope: <$250K
Better optics, detectors and layout for in vivo/in vitro experiments. Extensive customization (bringing other laser lines etc...)
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The MPScope Software Suite
Software choice for custom multiphoton microscope was limited:
- ScanImage (K. Svoboda's lab - Matlab)- LabView based software
MPScope:- Comprehensive suite of programs to control custom multiphotonmicroscopes and analyze results- Downloaded by ~ 50 laboratories worldwide (executable or source code)- Extensive community, now on NITRC- Commercial scopes using MPScope
Nguyen et al. (2006) MPScope: a versatile software suite for multiphoton microscopy. J. Neurosci. MethodsNguyen, Q.-T. and Kleinfeld, D. (2008) Book chapter in "In vivo optical imaging of brain function"
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MPScope: Description
MPScope =
MPScan
+
MPView
+
MPFileMicrosoft Windows Platform
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Important features of MPScope
High performance suite of software:
- Very fast, compact (native compiled code)- Symmetrical line scans for fast frame rate- Easy deployment: no need for run-time libraries- Professional looking GUI- Supports wide variety of microscope hardware- Multithreaded- Intel Integrated Performance Primitive Library
COM (Component Object Model) -based technologies:
- ActiveX Automation client and server- ActiveX Scripting- Structured Storage
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File Format Considerations
Goal of File Format :
Uncompromizing performance and seamless integration withWindows to allow different types of data (imaging, electrophys)to be stored
Native (i.e., binary with Intel byte ordering)- Fast- Opaque header
Text/XML-based data file:- Bulky (storing binary data is convoluted)- Slower
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The MPScope File Format (I)
Structured Storage: "A File System Inside a File"
- COM: Component Object Model (Windows)- Compound Files: Implementation of Structured Storage
Structured Storage
- Hierarchical organizations of folders and data streams insidea data file- Previously used as the Microsoft Office file format mechanism,CAD programs, etc...
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The MPScope File Format (II)"A File System Inside a File"
- Extensible file structure (displacement deltas)
- Allow e-phys, imaging + other info to be stored independently
- Queriable, extensible, programmableProperty Information Stream
Solves the opaque, non-extensible header problem!Data mining
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Interoperability with other applications (I)
Data Interchange Via Disk File
MPScan (acquisition):- Save as BMP file
MPView:- Save as: TIFF
AVIBMP
Convenient, but ackward and slow!
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Interoperability with other applications (II)
Data Interchange from adressing space to adressing space
- Faster, more accurate memory to memory transfer- ActiveX Automation + ActiveX Scripting
Possibilities:
- MPView -> Matlab (images to matrices automatically)One mouse click
- MPFile.OCX -> Matlab, Visual Basic, C++ clientsA few lines of code (high-level component)
- MPScan -> Header additions in near real-time
- MPScan -> MySQL database for logging files
- MPScan -> whole frames to clients in near real-time
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Interoperability with other applications (III)
The MPFILE.OCX component
- ActiveX Automation standard component
- Opens MPScope files from any ActiveX Automation- enabledapplication (Matlab, C/C++, Visual Basic, Delphi)
- High-level interface, no need to think about headers, file offsets
- Backward and forward compatible
-Easy to use (Matlab example):f = figure( [300, 300, 500, 500])mpfile = actxcontrol('MPFile.Data', [0, 0, 500, 500], f)openResult = invoke(mpfile, 'OpenMPFile', 'c:\MCC\050105_006.MPD')openResult =
0frameCount = invoke(mpfile, 'ReadParameter', 'Frame Count')frameCount =
150
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ConclusionWhat we learned:
It's OK to have a proprietary file format as long as there aresoftware translators for major image formats and softwarebridges to other applications.
Future Directions:
- Enhanced Windows Integration.
Thumbnail images in Explorer, Windows 64-bit - Cross-Platform Tools for Mac OSX and Linux.
Java libraries for reading Compound Files (Apache POIFS).
Compound File specs opened by Microsoft as part ofthe Microsoft Open Specification Promise (2007)