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<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>


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== Contents ==
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===General Lab Topics===
*[[Research Group Contact Info]]
*[[Conferences]]
*[[Journal Club]]
*[[Subject Recruitment]]
*[[Publications]]
*[[Documents]]
*[[Current Problems]]
*[[Archive]] Obsolete stuff here.
===Administration===
*[[Hardware Purchasing]]
*[[Laboratory Equipment List]]
===Scanco MicroCT===
----
* [[Project Management]]
* [[Evaluation]]
* [[Print outs and visualization]]
===VMS Workstations===
----
* [[VMS]]
: Basic usage of VMS systems.
* [[Scanco System and Setup]]
* [[Writing Scripts]]
* [[File Transfer]]
* [[Errors and Fixes]]
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===Visualization===
----
*[[Using ParaView]]
===Registration and Segmentation===
----
*[[Scanco Image Registration]]
*[[SimilarityRegistration]]
===Finite Element Modelling===
----
*[[Tutorial on Generating AIMs for FE Analysis]]
: First steps for processing microCT data for FE analysis.
*[[Tutorial on building an FE model with python and vtkski]]
: Read this if you want to build FE models from microCT data, particularly if you have unusual boundary conditions.
*[[Scanco Finite Element Modelling]]
: We typically use our own FE solver, faim.  This documentation may however be useful if you want for example to make comparisons with Scanco's FE solver.
===Statistics===
*[[JAGS Usage]]
: Analysis of Bayesian models using Markov Chain Monte Carlo
===Computers===
----
This section covers generic computer-related topics not covered in other sections.
*[[Unix command line basics]]
*[[ssh|Setting up Key Authentication for SSH]]
*[[Lab Server Configuration]]


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At this time, the major sections of this site are the [[How To's]] pages, for FAQs about various lab processes, and the [[Documents]] section where relevant documents have been uploaded.
===Developer===
----


====Lab Software Projects====
*[[Bone lab libraries]]
: A library of reusable bits for the kinds of things we do in the lab.  Built on VTK and ITK and other toolkits.
**[[vtkski development]]
**[[vtkMy development]]
*[[Bone lab applications]] provides a list of lab custom software.
*[[Writing Python scripts that use vtkski]]
*[[ParaView Extensions]]
: How to compile and use the lab ParaView Extensions.
*[[faim development]]
: FAIM is our finite element solver.
*[[SAP development]]
: SAP is a tool for visualizing and manipulating AIMs.


====Platforms====
Obtaining, compiling and installing software development tools on various systems.
*[[Development on OS-X]]
*[[Development for Linux]]
*[[Development on Windows]]
*[[Development on VMS]]


This is a user-based site, to be edited and improved by all users - feel free to make any modifications you see fit!
====Languages and Toolkits====
*See the [[Help:Contents| Help]] section for help using and adding to this site.  The [[Sandbox]] page has been added as a place to practice making changes, adding whatever you feel, to familiarize yourself with the 'Wiki' environment.
*[[C++ Development]]
*User accounts have been set up for everyone within the lab.  To see any pages other than this 'Main Page' or to edit any pages, you must login - click the Log-in tab at the top right of page.
*[[Creating VTK Classes]]
*[[ITK Development]]


====Development Tools====
*[[Subversion (SVN)]] for accessing the source code of lab software.


If you have any new problems or unanswered questions, post them on the [[Current Problems]] page.  Here, group members can post and discuss current problems.  Once problems have been solved, they should be converted into a "How To" format and placed appropriately within the How To section.
===Miscellaneous===
----
*[[Wireless Network in Morphometrics Lab]]


And here, we have recently added the [[Publications]] section where all of the lab's publications are posted with the pdf's.
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Revision as of 14:12, 16 September 2010


Bone Imaging Laboratory Wiki


Wiki Concept

The idea of the 'Wiki' site is that any authorized user, in this case a member of the lab, can see and edit any of the pages on this site. Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group.

The purpose of this is to facilitate information exchange within the lab and keep up-to-date HowTo and User Manuals for all lab procedures.

Contents

General Lab Topics

Administration

Scanco MicroCT

VMS Workstations

Basic usage of VMS systems.

Visualization

Registration and Segmentation

Finite Element Modelling

First steps for processing microCT data for FE analysis.
Read this if you want to build FE models from microCT data, particularly if you have unusual boundary conditions.
We typically use our own FE solver, faim. This documentation may however be useful if you want for example to make comparisons with Scanco's FE solver.

Statistics

Analysis of Bayesian models using Markov Chain Monte Carlo

Computers

This section covers generic computer-related topics not covered in other sections.

Developer

Lab Software Projects

A library of reusable bits for the kinds of things we do in the lab. Built on VTK and ITK and other toolkits.
How to compile and use the lab ParaView Extensions.
FAIM is our finite element solver.
SAP is a tool for visualizing and manipulating AIMs.

Platforms

Obtaining, compiling and installing software development tools on various systems.

Languages and Toolkits

Development Tools

Miscellaneous


A link back to: Steve Boyd's homepage

To return to the Lab home page: Biomedical Imaging Metrics Homepage
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