Difference between revisions of "Main Page"

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__NOTOC__
 
__NOTOC__
 
 
<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
 
<center><b><font size="+3">Bone Imaging Laboratory Wiki</font></b>
 
  
  
 
<table width="97%" border="0">
 
<table width="97%" border="0">
 
<tr>  
 
<tr>  
<td width="450" align="left" valign="middle" bgcolor="#ccff66">
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<td width="200" align="center" valign="middle" bgcolor="#ccff66">
 
<div align="center"><b><u> Wiki Concept</u></b></div>
 
<div align="center"><b><u> Wiki Concept</u></b></div>
  
<P>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, as well as create new pages as required.  
+
<P> <br>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, as well as create new pages as required.  
 
Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group.</P>  
 
Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group.</P>  
<p>The purpose of this is to facilitate
+
 
information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.</P>
+
</td>
 +
 
 +
<td bgcolor="#ccff66">      [[File:BonelabScanners.JPG|center|700px]]</td>
 +
 
 +
<td width="200" align="center" valign="middle" bgcolor="#ccff66">
 +
<div align="center"><b><u> The Purpose</u></b></div>
 +
 
 +
<p><br>It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.</P>
 
</td>
 
</td>
  
<td bgcolor="#ccff05">[[Image:Smaller_bone_loss.jpg]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</table>
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</center>
 
</center>
  
== Contents ==
 
 
{| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2"
 
{| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2"
 
|-
 
|-
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|valign="top"|
 
|valign="top"|
  
===[[Scanco User Instructions]]===
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==[[Scanco User Instructions]]==
----
 
 
[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
 
[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
 
*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
 
*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
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*[[Scanco_User_Instructions#Image_Data| Image Data]]
 
*[[Scanco_User_Instructions#Image_Data| Image Data]]
 
*[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]
 
*[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]
 
[[Scanco_User_Instructions#Bone_Morphometry_and_Densitometry| '''Bone Morphometry and Densitometry''']]
 
*[[Scanco_User_Instructions#Suggested_readings| Suggested readings]]
 
*[[Scanco_User_Instructions#Model-Independent_.28Direct.29_Structural_Measurements| Model-Independent (Direct) Structural Measurements]]
 
*[[Scanco_User_Instructions#Densitometric_Measurements| Densitometric Measurements]]
 
  
 
[[Scanco_User_Instructions#Scanning| '''Scanning''']]
 
[[Scanco_User_Instructions#Scanning| '''Scanning''']]
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*[[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29| Scan Parameters (Controlfiles)]]
 
*[[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29| Scan Parameters (Controlfiles)]]
 
*[[Scanco_User_Instructions#Perform_a_Scan| Perform a Scan]]
 
*[[Scanco_User_Instructions#Perform_a_Scan| Perform a Scan]]
*[[Scanco_User_Instructions#Image_Artifacts| Image Artifacts]]
+
*[[Scanco_User_Instructions#Action_on_Image_Artifacts| Action on Image Artifacts]]
  
 
[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
 
[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
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[[Scanco_User_Instructions#Results| '''Results''']]
 
[[Scanco_User_Instructions#Results| '''Results''']]
 
*[[Scanco_User_Instructions#Images_and_Animations| Images and Animations]]
 
*[[Scanco_User_Instructions#Images_and_Animations| Images and Animations]]
 +
*[[Scanco_User_Instructions#Image_Tours| Image Tours]]
 
*[[Scanco_User_Instructions#Extract_Results| Extract Results]]
 
*[[Scanco_User_Instructions#Extract_Results| Extract Results]]
 
*[[Scanco_User_Instructions#Generate_Report| Generate Report]]
 
*[[Scanco_User_Instructions#Generate_Report| Generate Report]]
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*[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
 
*[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
 
*[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]
 
*[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]
 
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
===[[Scanco Administration]]===
+
==[[Scanco Administration]]==
----
 
 
[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
 
[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
 
*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
 
*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
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*[[Scanco_Administration#System_Updates| System Updates]]
 
*[[Scanco_Administration#System_Updates| System Updates]]
 
*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
 
*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
*[[Scanco_Administration#Beam_Hardening_Correction_.28BHC.29| Beam Hardening Correction (BHC)]]
 
 
*[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]
 
*[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]
  
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*[[Scanco_Administration#Manipulate_RSQ| Manipulate RSQ]]
 
*[[Scanco_Administration#Manipulate_RSQ| Manipulate RSQ]]
 
*[[Scanco_Administration#Manipulate_ISQ| Manipulate ISQ]]
 
*[[Scanco_Administration#Manipulate_ISQ| Manipulate ISQ]]
 +
*[[Scanco_Administration#Image_Artifacts| Image Artifacts]]
  
 
[[Scanco_Administration#Evaluation| '''Evaluation''']]
 
[[Scanco_Administration#Evaluation| '''Evaluation''']]
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*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
 
*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
 
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
 
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
*[[Scanco_Administration#Setup_other_remote_access| Setup other remote access]]
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*[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]]
 
*[[Scanco_Administration#Physical_connections| Physical connections]]
 
*[[Scanco_Administration#Physical_connections| Physical connections]]
  
 
[[Scanco_Administration#Dose| '''Dose''']]
 
[[Scanco_Administration#Dose| '''Dose''']]
 
*[[Scanco_Administration#Dose_Calculations| Dose Calculations]]
 
*[[Scanco_Administration#Dose_Calculations| Dose Calculations]]
*[[Scanco_Administration#Scan_Protocols_for_Low_Dose| Scan Protocols for Low Dose]]
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*[[Scanco_Administration#Optimize_Scan_for_Low_Dose| Optimize Scan for Low Dose]]
 
 
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
===[[Image Registration]]===
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==[[Xradia Instructions]]==
----
+
*[[Xradia_Instructions#User_Tutorials| User Tutorials]]
 +
*[[Xradia_Instructions#Scanning| Scanning]]
 +
*[[Xradia_Instructions#Reconstruction| Reconstruction]]
 +
*[[Xradia_Instructions#Special_Topics| Special Topics]]
 +
*[[Xradia_Instructions#Image_Tours| Image Tours]]
 +
 
 +
==[[Books and References]]==
 +
[[Books_and_References#Imaging|'''Imaging''']]
 +
*[[Books_and_References#Essential_Physics_of_Medical_Imaging| Essential Physics of Medical Imaging]]
 +
 
 +
[[Books_and_References#Bone|'''Bone''']]
 +
*[[Books_and_References#Books_on_Bone| Books on Bone]]
 +
*[[Books_and_References#Bone_Morphometry_and_Densitometry| Bone Morphometry and Densitometry]]
 +
 
 +
[[Books_and_References#Student_Reports|'''Student Reports''']]
 +
 
 +
==[[Image Registration]]==
 
[[Image_Registration#Scanco_Image_Registration|'''Scanco Image Registration''']]
 
[[Image_Registration#Scanco_Image_Registration|'''Scanco Image Registration''']]
 
*[[Image_Registration#Image_Transformation|Image Transformation]]
 
*[[Image_Registration#Image_Transformation|Image Transformation]]
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*[[Image_Registration#ITK_Rigid_registration_for_HR-pQCT| ITK Rigid registration for HR-pQCT]]
 
*[[Image_Registration#ITK_Rigid_registration_for_HR-pQCT| ITK Rigid registration for HR-pQCT]]
  
===[[Finite Element Modelling]]===
+
==[[Finite Element Modelling]]==
----
+
*[[Finite_Element_Modelling#Scanco_Finite_Element_Modelling| Scanco Finite Element Modelling]]
 
*[[Finite_Element_Modelling#FAIM_Finite_Element_Solver| FAIM Finite Element Solver]]
 
*[[Finite_Element_Modelling#FAIM_Finite_Element_Solver| FAIM Finite Element Solver]]
 +
*[[Finite_Element_Modelling#FE_Tutorial| FE Tutorial]]
 
*[[Finite_Element_Modelling#Prepare_AIMs_for_FE_Analysis| Prepare AIMs for FE Analysis]]
 
*[[Finite_Element_Modelling#Prepare_AIMs_for_FE_Analysis| Prepare AIMs for FE Analysis]]
*[[Finite_Element_Modelling#Scanco_Finite_Element_Modelling| Scanco Finite Element Modelling]]
 
  
===Developer===
+
==[[Software Plugins and Codes]]==
 
----
 
----
 +
*[[Software_Plugins_and_Codes#ImageJ| '''ImageJ''']]
 +
*[[Software_Plugins_and_Codes#Amira| '''Amira''']]
 +
*[[Software_Plugins_and_Codes#R|'''R''']]
 +
*[[Software_Plugins_and_Codes#ParaView| '''ParaView''']]
  
====[[Software Plugins and Codes]]====
+
==Languages and Toolkits==
----
+
*[[C++|'''C++''']]
* [[Software_Plugins_and_Codes#ImageJ_Plugin_for_AIM_ISQ_RSQ_files| ImageJ Plugin for AIM ISQ RSQ files]]
+
*[[VTK|'''VTK''']]
* [[Software_Plugins_and_Codes#Amira_Script_for_AIM_files| Amira Script for AIM files]]
+
*[[ITK|'''ITK''']]
*[[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.
 
*[[Bone lab applications]] provides a list of lab custom software.
 
*[[SAP development]]
 
: SAP is a tool for visualizing and manipulating AIMs.
 
*[[IGFA control]]
 
: Image guided failure assessment device (aka the cannon) can be controlled from PC via serial port.
 
*[[JAGS Statistics]]
 
: Analysis of Bayesian models using Markov Chain Monte Carlo
 
*[[ParaView]]
 
*[[Subversion (SVN)]] for accessing the source code of lab software.
 
 
 
====Platforms====
 
----
 
Obtaining, compiling and installing software development tools on various systems.
 
*[[Development on OS-X]]
 
*[[Development for Linux]]
 
*[[Development on Windows]]
 
*[[Development on OpenVMS]]
 
  
====Languages and Toolkits====
+
==Miscellaneous==
----
+
*[[Software_Development_Platforms| '''Software Development Platforms''']]
*[[C++ Development]]
+
*[[Archive|'''Archive''']]  
*[[Creating VTK Classes]]
 
*[[ITK Development]]
 
*[[Matlab Development]]
 
*[[Writing plugins for ParaView]]
 
  
===Miscellaneous===
 
----
 
*[[Archive]] Obsolete stuff here.
 
This section covers generic computer-related topics not covered in other sections.
 
*[[Unix command line basics]]
 
*[[ssh|SSH tricks]]
 
*[[Lab Server Configuration]]
 
 
|}
 
|}
 
  
 
----
 
----
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<tr>
 
<tr>
 
<td align="left" valign="middle" >
 
<td align="left" valign="middle" >
A link back to: [http://www.enme.ucalgary.ca/~skboyd/ Steve Boyd's homepage]
+
To: [https://www.ucalgary.ca/labs/bonelab/team/steven-boyd '''Steve Boyd's homepage''']
 
</td>
 
</td>
<td align="left" valign="middle"> To return to the Lab home page: [http://www.enme.ucalgary.ca/research/microct/ Biomedical Imaging Metrics Homepage]</td>
+
<td align="left" valign="middle"> To: [https://www.ucalgary.ca/labs/bonelab/home '''Bone Imaging Lab homepage''']</td>
 
</tr></table>
 
</tr></table>

Revision as of 16:02, 22 January 2021

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, as well as create new pages as required. Also, there is a document section where useful documents can uploaded or downloaded by anyone in the group.

BonelabScanners.JPG
The Purpose


It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.

Scanco User Instructions

OpenVMS Basics

Micro-CT Basics

Scanning

Evaluation

Results

Data Management

Import and Export

Remote Access

Scanco Administration

OpenVMS

Calibration and QC

Scanning

Evaluation

Results

Data Management

Process, Printer and System

Remote Access

Dose

Xradia Instructions

Books and References

Imaging

Bone

Student Reports

Image Registration

Scanco Image Registration

SimilarityRegistration

skiRegistration

Finite Element Modelling

Software Plugins and Codes


Languages and Toolkits

Miscellaneous


To: Steve Boyd's homepage

To: Bone Imaging Lab homepage