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Software
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Seminars and Reading Groups
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= The CMIC Group = = The CMIC Group =
== Administration == == Administration ==
-For any queries regarding the administration of CMIC please contact Ron Gaston on Ext. 30221. Ron is located in room 4.13+For any queries regarding the administration of CMIC please contact Ron Gaston on Ext. 30221. Ron is located in room 3.09 of the Engineering Front Building
Requests for a Wiki user name and password should be sent to [mailto:R.Gaston@ucl.ac.uk Ron]. Requests for a Wiki user name and password should be sent to [mailto:R.Gaston@ucl.ac.uk Ron].
-Holiday request form: [[Media:leave-form.pdf]]+'''PowerPoint Poster templates:'''
 + 
 +A0 Portrait PowerPoint 97/2003 [[Media:CMIC-powerpoint-template-A0-portrait.ppt]].
 +
 +A0 Landscape PowerPoint 97/2003 [[Media:CMIC-powerpoint-template-A0-landscape.ppt]]. WIKI Media messes up the formatting when uploading the file. Please reposition the CMIC logo to the bottom right hand corner of the poster.
 +
 + 
 + 
 +HCMIC Logo vector file: [[Media:cmic-logo.pdf]]
Room bookings: [http://www.cs.ucl.ac.uk/cgi-bin/roombooking/ CS] Room bookings: [http://www.cs.ucl.ac.uk/cgi-bin/roombooking/ CS]
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Voicemail quick reference: [[Media:VoiceMailQR.pdf]] (from Mark White); see [http://www.ucl.ac.uk/efd/telecoms/voicemail/ UCL voicemail page] for official manual, forms etc. Voicemail quick reference: [[Media:VoiceMailQR.pdf]] (from Mark White); see [http://www.ucl.ac.uk/efd/telecoms/voicemail/ UCL voicemail page] for official manual, forms etc.
 +
 +== Funding ==
 +For the latest funding opportunities: UCL colleagues are encouraged to sign up for the Research Strategy Forum mailing list at https://www.mailinglists.ucl.ac.uk/mailman/listinfo/beams-research-board. The BEAMS research facilitators produce a document each month detailing the funding opportunities that are currently available. These will appear here.
 +
 +Funding Opportunities August 2011 [[media:BEAMS Sucesses and Opportunities - August 2011 (2).pdf]].
 +
 +The EPSRC have changed the way they are funding Fellowships. Please see the Faculty of Engineering for more details. Matt Davies, research facilitator for BEAMS, gave a very informative presentation on the changes the EPSRC have introduced. Please follow the links below.
 +
 +EPSRC Fellowship Briefing (EPSRC slides) [[media:EPSRC Fellowships Briefing August 2011.ppt]].
 +
 +EPSRC Fellowship Briefing (UCL slides) [[media:EPSRC Briefing Presentation on Fellowships_UCL.ppt]].
 +
 +For an in-depth guide to EPSRC fellowships please read: [[media:BEAMS Fellowships guide_Early career v1.pdf]].
== People == == People ==
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* [[Image-Guided Intervention Workshops]]. * [[Image-Guided Intervention Workshops]].
 +
 +* [[Tomography Interest Group]].
 +
 +* [[IGI Journal Club]].
= Software = = Software =
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* [[Boost Libraries]] * [[Boost Libraries]]
* [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping. * [http://www.cs.ucl.ac.uk/research/medic/camino/ Camino] Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.
 +* [[dcmtk]] a collection of libraries and applications implementing large parts the DICOM standard.
* [[FFTW]] C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST). * [[FFTW]] C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
* [[FLTK]] Fast Light Toolkit * [[FLTK]] Fast Light Toolkit
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* [[latex2html]] Perl program to convert latex to html [http://www.latex2html.org] * [[latex2html]] Perl program to convert latex to html [http://www.latex2html.org]
* [[Matlab]] Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc. * [[Matlab]] Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc.
 +* [[niftkAffine]] NifTK intensity based rigid or affine registration
* [http://cmicdev.cs.ucl.ac.uk/trac/browser/trunk/matlab Matlab Function Repository] Matlab Functions for Image Processing and File I/O. * [http://cmicdev.cs.ucl.ac.uk/trac/browser/trunk/matlab Matlab Function Repository] Matlab Functions for Image Processing and File I/O.
 +* [[ParaView]] is an open-source, multi-platform data analysis and visualization application.
* [[Perl OpenOffice::OODoc]] OpenOffice package for Perl - enables generation of Office documents, such as slideshows from Perl scripts. * [[Perl OpenOffice::OODoc]] OpenOffice package for Perl - enables generation of Office documents, such as slideshows from Perl scripts.
* [[SPM]] Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images. * [[SPM]] Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images.
* [[SSH]] * [[SSH]]
 +* Subversion Version Control Software: [http://svnbook.red-bean.com/en/1.5/index.html Online Manual] and [[Media:Svn-book.pdf|PDF Book]].
* [[TetGen]] "A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator." * [[TetGen]] "A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator."
* [http://math.nist.gov/tnt/ TNT] C++ templated matrix classes. * [http://math.nist.gov/tnt/ TNT] C++ templated matrix classes.
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* [[Nifti]] * [[Nifti]]
* There are a number of fairly complete descriptions of deformation and image formats used at CMIC on the [http://cmicdev.cs.ucl.ac.uk/trac Trac wiki]. * There are a number of fairly complete descriptions of deformation and image formats used at CMIC on the [http://cmicdev.cs.ucl.ac.uk/trac Trac wiki].
 +* [http://www.dclunie.com/medical-image-faq/html Medical Image FAQ]
 +
 += Conference Proceedings =
 +
 +A directory containing the electronic copies of the conference proceedings can be found at: /cs/research/cmic/conf-proc.
= [[FAQ]] = = [[FAQ]] =
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Pages for specific projects at CMIC. Pages for specific projects at CMIC.
-* [[Mammo Group]]+* [[Mammo Group|Breast Cancer Imaging]]
* [[CMIC Cluster]] Sunfire Cluster - Comic100 * [[CMIC Cluster]] Sunfire Cluster - Comic100
* [[Moving Liver]] * [[Moving Liver]]

Current revision

This is the UCL Centre for Medical Image Computing (CMIC) wiki. The official CMIC webpage is here.

Contents

[edit]

The CMIC Group

[edit]

Administration

For any queries regarding the administration of CMIC please contact Ron Gaston on Ext. 30221. Ron is located in room 3.09 of the Engineering Front Building

Requests for a Wiki user name and password should be sent to Ron.

PowerPoint Poster templates:

A0 Portrait PowerPoint 97/2003 Media:CMIC-powerpoint-template-A0-portrait.ppt.

A0 Landscape PowerPoint 97/2003 Media:CMIC-powerpoint-template-A0-landscape.ppt. WIKI Media messes up the formatting when uploading the file. Please reposition the CMIC logo to the bottom right hand corner of the poster.


HCMIC Logo vector file: Media:cmic-logo.pdf

Room bookings: CS UCL Med Phys

Voicemail quick reference: Media:VoiceMailQR.pdf (from Mark White); see UCL voicemail page for official manual, forms etc.

[edit]

Funding

For the latest funding opportunities: UCL colleagues are encouraged to sign up for the Research Strategy Forum mailing list at https://www.mailinglists.ucl.ac.uk/mailman/listinfo/beams-research-board. The BEAMS research facilitators produce a document each month detailing the funding opportunities that are currently available. These will appear here.

Funding Opportunities August 2011 media:BEAMS Sucesses and Opportunities - August 2011 (2).pdf.

The EPSRC have changed the way they are funding Fellowships. Please see the Faculty of Engineering for more details. Matt Davies, research facilitator for BEAMS, gave a very informative presentation on the changes the EPSRC have introduced. Please follow the links below.

EPSRC Fellowship Briefing (EPSRC slides) media:EPSRC Fellowships Briefing August 2011.ppt.

EPSRC Fellowship Briefing (UCL slides) media:EPSRC Briefing Presentation on Fellowships_UCL.ppt.

For an in-depth guide to EPSRC fellowships please read: media:BEAMS Fellowships guide_Early career v1.pdf.

[edit]

People

People at CMIC. Please enter your phone numbers, email address, room number, and whatever else at this address. There's also a staff page on the external website which is useful for finding contact details.

[edit]

PhD

[edit]

Seminars and Reading Groups

Information on seminars at CMIC.

  • ImPr Pages Informal seminars on image processing.
[edit]

Software

Information on software used, (or which could be used) at CMIC. See also the CMIC software development Trac wiki.

  • Acell Details about Bill Crum's analysis of cell images (Updated August 2007).
  • Boost Libraries
  • Camino Software package for analysis and reconstruction of Diffusion MRI data, tractography and connectivity mapping.
  • dcmtk a collection of libraries and applications implementing large parts the DICOM standard.
  • FFTW C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
  • FLTK Fast Light Toolkit
  • Fluid Registration Details about Bill Crum's fluid implementation and related tools (Updated August 2007).
  • FSL Toolbox/library for functional and structural neuroimaging analysis, written in C/C++. Popular tools include FLIRT, BET, and FAST.
  • FreeSurfer Cortical surface extraction, sub-cortical structure segmentation and inter-subject registration (FreeSurfer includes N3 bias correction)
  • giflib library for reading and writing gif images.
  • glpk The Gnu Linear Programming Kit
  • Grace Graph drawing program and library
  • GraphicsMagick Image manipulation software for common computer graphics image formats
  • gxv, DisplayVectorField2D, DisplayVectorField3D GIPL X Viewers. Programs to enable display of up to 3 images and overlayed vector fields.
  • imlib2 'X' image display routines.
  • Insight Toolkit [1] (ITK) C++ imaging and image processing, registration, algorithms classes.
  • ITK++ C++ Daniel and Julia's image processing and registration classes
  • latex2html Perl program to convert latex to html [2]
  • Matlab Numerical linear algebra software, with toolboxes for image processing, stats, optimisation, etc.
  • niftkAffine NifTK intensity based rigid or affine registration
  • Matlab Function Repository Matlab Functions for Image Processing and File I/O.
  • ParaView is an open-source, multi-platform data analysis and visualization application.
  • Perl OpenOffice::OODoc OpenOffice package for Perl - enables generation of Office documents, such as slideshows from Perl scripts.
  • SPM Matlab toolbox for segmentation, spatial normalisation, and voxel-wise statistical analysis of brain images.
  • SSH
  • Subversion Version Control Software: Online Manual and PDF Book.
  • TetGen "A Quality Tetrahedral Mesh Generator and Three-Dimensional Delaunay Triangulator."
  • TNT C++ templated matrix classes.
  • TOAST Martin and Simon's finite element solvers and tools in C++.
  • Virtual Network Computing (VNC) Desktop sharing system, for remote working, demos etc.
  • VTK C++ visualisation classes (some sort of interface to OpenGL).
  • vtkCmic Mark and David's classes for registration etc.
  • xfig Drawing program for the X Windows system.


[edit]

Image File Formats

  • Image File Formats Software available to read and manipulate image file formats and DICOM images in particular.
  • Nifti
  • There are a number of fairly complete descriptions of deformation and image formats used at CMIC on the Trac wiki.
  • Medical Image FAQ
[edit]

Conference Proceedings

A directory containing the electronic copies of the conference proceedings can be found at: /cs/research/cmic/conf-proc.

[edit]

FAQ

[edit]

Discussion

Discussion on a new CMIC Wiki / web pages

[edit]

Projects

Pages for specific projects at CMIC.

[edit]

Science-div

[edit]

Useful links

[edit]

Ethics

[edit]

Deadlines

  • Deadlines - Details of upcoming conference deadlines.
[edit]

Undergraduate and MSc Projects

UGprojectDA on Parallel computing for the reconstruction of magnetic resonance images.

[edit]

Postgraduate

[edit]

Reading Material

Reading Material (publicly readable)

Please see documentation on customizing the interface and the User's Guide for usage and configuration help.

Retrieved from "http://web4.cs.ucl.ac.uk/research/medic/cmic-wiki/index.php/Main_Page"