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__NOTOC__
 
__NOTOC__
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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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<table width="100%" border="0">
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<table width="97%" border="0">
 
 
<tr>  
 
<tr>  
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<td width="450" align="left" valign="middle" bgcolor="#ccff66">
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<td width="15%" 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> 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>
−
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
+
<br>
−
information exchange within the lab and keep up-to-date How To and User Manuals for all lab procedures.</P>
+
 
 +
<div align="center"><b><u> The Purpose</u></b></div>
 +
 
 +
<p>It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for lab's technical procedures and FAQ.</P>
 +
 
 +
</td>
 +
 
 +
<td bgcolor="#ccff66">      [[File:BonelabScanners.JPG|center|750px]]</td>
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 +
<td width="25%" align="left" valign="middle" bgcolor="#ccff66">
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<div align="center"><b><u> Read me</u></b></div>
 +
 
 +
<p>
 +
#Use '''Ctr+F''' to search within any page.
 +
#Never include login credentials especially password anywhere.
 +
#It's all users' responsibility to keep the info precise, updated, abundant, and useful, through editing/addition/deletion as needed by clicking [edit] on the top-right corner of a page or item. This includes combining same/similar topics besides an item whenever appropriate.
 +
#Add a redirect line after each new item for consistency:
 +
#:[[Image:Redirect.jpg|15px]] [[#top|''Return to Contents'']] or [[Main_Page|''Return to Main Page'']]
 +
#Click '''Help''' on navigation list on the left penal for detailed editing instructions.
 +
#Contact Ying if you are not sure where to put a new item or could not find an item.
 +
</P>
 
</td>
 
</td>
  
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<td bgcolor="#ccff05">[[Image:Smaller_bone_loss.jpg]]</td>
 
 
</tr>
 
</tr>
 
</table>
 
</table>
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</center>
 
</center>
  
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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"|
  
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== Contents ==
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==[[Scanco User Instructions]]==
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{| border="0" align="center" width="98%" valign="top" cellspacing="7" cellpadding="2"
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[[Scanco_User_Instructions#OpenVMS_Basics| '''OpenVMS Basics''']]
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|-
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*[[Scanco_User_Instructions#OpenVMS_Beginner.27s_Reference| Beginner's Reference]]
−
! width="33%"|
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*[[Scanco_User_Instructions#Session_Manager| Session Manager]]
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! |
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*[[Scanco_User_Instructions#DEC_Terminal_and_Digital_Command_Language_.28DCL.29| DEC Terminal and DCL]]
−
! width="33%"|
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*[[Scanco_User_Instructions#DCL_Programming_Guide| DCL Programming Guide]]
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! |
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*[[Scanco_User_Instructions#List_of_basic_commands| List of basic commands]]
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! width="33%"|
 
−
|-
 
−
|valign="top"|
 
  
−
===General Lab Topics===
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[[Scanco_User_Instructions#Micro-Computed_Tomography_.28.C2.B5CT.29_Basics| '''Micro-CT Basics''']]
−
----
+
*[[Scanco_User_Instructions#User_Tutorials| User Tutorials]]
−
*[[Research Group Contact Info]]
+
*[[Scanco_User_Instructions#Micro-CT_Image_Basics| µCT Image Basics]]
−
*[[Conferences]]
+
*[[Scanco_User_Instructions#Image_Data| Image Data]]
−
*[[Journal Club]]
+
*[[Scanco_User_Instructions#Scanco_Medical_Micro-CT_Software| Scanco Medical µCT Software]]
−
*[[Subject Recruitment]]
 
−
*[[Publications]]
 
−
*[[Documents]]
 
−
*[[Current Problems]]
 
−
*[[Suggested Improvements to BME]]
 
  
−
===Lab Administration===
+
[[Scanco_User_Instructions#Scanning| '''Scanning''']]
−
----
+
*[[Scanco_User_Instructions#Sample_Name_Convention| Sample Name Convention]]
−
*[[Hardware Purchasing]]
+
*[[Scanco_User_Instructions#Register_Samples_for_Scanning| Register Samples for Scanning]]
−
*[[Laboratory Equipment List]]
+
*[[Scanco_User_Instructions#Log_Sheets| Log Sheets]]
 +
*[[Scanco_User_Instructions#Patient_Casts_and_Sample_Holders| Patient Casts and Sample Holders]]
 +
*[[Scanco_User_Instructions#Scan_Parameters_.28Controlfiles.29| Scan Parameters (Controlfiles)]]
 +
*[[Scanco_User_Instructions#Perform_a_Scan| Perform a Scan]]
 +
*[[Scanco_User_Instructions#Action_on_Image_Artifacts| Action on Image Artifacts]]
  
−
===Scanco MicroCT and VMS Workstations===
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[[Scanco_User_Instructions#Evaluation| '''Evaluation''']]
−
----
+
*[[Scanco_User_Instructions#Evaluate_a_Scan| Evaluate a Scan]]
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* [http://www.ucalgary.ca/microct/documents/x-ray_how_to Detailed OpenVMS and Scanco MicroCT Instructions]
+
*[[Scanco_User_Instructions#Draw_Contours| Draw Contours]]
−
* [[Project Management]]
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*[[Scanco_User_Instructions#Evaluation_Scripts| Evaluation Scripts]]
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* [[OpenVMS]]
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*[[Scanco_User_Instructions#Image_Processing_Language_.28IPL.29_Scripting| IPL Scripting]]
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: Basic usage of OpenVMS systems.
 
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* [[Scanco MicroCT Operation]]
 
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* [[MicroCT Evaluation and Analysis]]
 
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* [[Writing IPL Scripts]]
 
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* [[Errors and Fixes]]
 
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* [[Scanco Medical FAQ]]
 
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* [[Uploading MRI to Scanco]]
 
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* [[Uploading Xradia *.bin to Scanco]]
 
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* [[Remote access to MicroCT system (working from home)]]
 
  
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===Dual-energy X-ray absorptiometry (DXA)===
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[[Scanco_User_Instructions#Results| '''Results''']]
−
----
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*[[Scanco_User_Instructions#Images_and_Animations| Images and Animations]]
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* [[Scanning guidelines]]
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*[[Scanco_User_Instructions#Image_Tours| Image Tours]]
 +
*[[Scanco_User_Instructions#Extract_Results| Extract Results]]
 +
*[[Scanco_User_Instructions#Generate_Report| Generate Report]]
  
−
===Network Access===
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[[Scanco_User_Instructions#Data_Management| '''Data Management''']]
−
----
+
*[[Scanco_User_Instructions#Trainee.E2.80.99s_Data_Responsibility| Trainee’s Data Responsibility]]
−
* [[VPN Setup]]
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*[[Scanco_User_Instructions#Move_data_from_Data_Disk_to_Project_Disk| Move data from Data Disk to Project Disk]]
  
 +
[[Scanco_User_Instructions#Import_and_Export| '''Import and Export''']]
 +
*[[Scanco_User_Instructions#Import_Foreign_Data_to_Scanco_System| Import Foreign Data]]
 +
*[[Scanco_User_Instructions#Import_MRI_to_Scanco_System| Import MRI Images]]
 +
*[[Scanco_User_Instructions#Import_Xradia_.2A.bin_to_Scanco_System|Import Xradia *.bin]]
 +
*[[Scanco_User_Instructions#Get_Your_Files| Get Your Files]]
  
 +
[[Scanco_User_Instructions#Remote_Access| '''Remote Access''']]
 +
*[[Scanco_User_Instructions#VPN_Setup| VPN Setup]]
 +
*[[Scanco_User_Instructions#Setup_for_MAC.2FLinux| Setup for MAC/Linux]]
 +
*[[Scanco_User_Instructions#Setup_for_Windows| Setup for Windows]]
 +
*[[Scanco_User_Instructions#Remote_Access_FAQ| Remote Access FAQ]]
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
−
===Registration and Segmentation===
+
==[[Scanco Administration]]==
−
----
+
[[Scanco_Administration#OpenVMS| '''OpenVMS''']]
−
*[[Scanco Image Registration]]
+
*[[Scanco_Administration#OpenVMS_References| OpenVMS References]]
−
*[[SimilarityRegistration]]
+
*[[Scanco_Administration#Unix_related| Unix related]]
−
*[[skiRegistration]]
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*[[Scanco_Administration#Graphical_Applications| Graphical Applications]]
−
*[[MRI to HR-pQCT Registration with Scanco]]
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*[[Scanco_Administration#File_Operations| File Operations]]
 +
*[[Scanco_Administration#Administrative_Commands| Administrative Commands]]
 +
 
 +
[[Scanco_Administration#Calibration_and_QC | '''Calibration and QC''']]
 +
*[[Scanco_Administration#System_Updates| System Updates]]
 +
*[[Scanco_Administration#Calibration_and_Conversion| Calibration and Conversion]]
 +
*[[Scanco_Administration#Quality_Control_.28QC.29| Quality Control (QC)]]
 +
 
 +
[[Scanco_Administration#Scanning| '''Scanning''']]
 +
*[[Scanco_Administration#Scanner_User_Manual| Scanner User Manual]]
 +
*[[Scanco_Administration#Scanco.27s_FAQ| Scanco's FAQ]]
 +
*[[Scanco_Administration#Scan| Scan]]
 +
*[[Scanco_Administration#Reconstruction| Reconstruction]]
 +
*[[Scanco_Administration#Manipulate_RSQ| Manipulate RSQ]]
 +
*[[Scanco_Administration#Manipulate_ISQ| Manipulate ISQ]]
 +
*[[Scanco_Administration#Image_Artifacts| Image Artifacts]]
 +
 
 +
[[Scanco_Administration#Evaluation| '''Evaluation''']]
 +
*[[Scanco_Administration#Analysis_Topics| Analysis Topics]]
 +
*[[Scanco_Administration#UCT_EVALUATION| UCT_EVALUATION]]
 +
*[[Scanco_Administration#Evaluation_FAQ| Evaluation FAQ]]
 +
*[[Scanco_Administration#IPL_FAQ| IPL FAQ]]
 +
 
 +
[[Scanco_Administration#Results| '''Results''']]
 +
*[[Scanco_Administration#Extract_Results| Extract Results]]
 +
*[[Scanco_Administration#Database| Database]]
 +
*[[Scanco_Administration#Other_FAQ| Other FAQ]]
  
−
===Finite Element Modelling===
+
[[Scanco_Administration#Data_Management | '''Data Management''']]
−
----
+
*[[Scanco_Administration#Lab.E2.80.99s_Data_Responsibility| Lab’s Data Responsibility]]
−
*[[FAIM Finite Element Solver]]
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*[[Scanco_Administration#HP_Server_and_Disk_Array| HP Server and Disk Array]]
−
: This is the lab finite element software.
+
*[[Scanco_Administration#Tape| Tape]]
−
*[[Tutorial on Generating AIMs for FE Analysis]]
+
*[[Scanco_Administration#USB_Drive| USB_Drive]]
−
: First steps for processing microCT data for FE analysis.
+
*[[Scanco_Administration#CDROM| CDROM]]
−
*[[Scanco Finite Element Modelling]]
+
*[[Scanco_Administration#Saveset_and_Zip_files| Saveset and Zip files]]
−
: 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.
+
*[[Scanco_Administration#Backup_and_Archive| Backup and Archive]]
  
−
===Visualization===
+
[[Scanco_Administration#Process.2C_Printer_and_System| '''Process, Printer and System''']]
−
----
+
*[[Scanco_Administration#Processes_and_Jobs| Processes and Jobs]]
−
*[[Using ParaView]]
+
*[[Scanco_Administration#Printer| Printer]]
 +
*[[Scanco_Administration#System| System]]
  
−
===Statistics===
+
[[Scanco_Administration#Remote_Access|'''Remote Access''']]
−
----
+
*[[Scanco_Administration#For_Scanco_support| For Scanco support]]
−
*[[JAGS Usage]]
+
*[[Scanco_Administration#Access_VMS_filesystem| Access VMS filesystem]]
−
: Analysis of Bayesian models using Markov Chain Monte Carlo
+
*[[Scanco_Administration#Setup_remote_access_FAQ| Setup remote access FAQ]]
 +
*[[Scanco_Administration#Physical_connections| Physical connections]]
  
−
===Computers===
+
[[Scanco_Administration#Dose| '''Dose''']]
−
----
+
*[[Scanco_Administration#Dose_Calculations| Dose Calculations]]
−
This section covers generic computer-related topics not covered in other sections.
+
*[[Scanco_Administration#Optimize_Scan_for_Low_Dose| Optimize Scan for Low Dose]]
−
*[[Unix command line basics]]
 
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*[[ssh|SSH tricks]]
 
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*[[Lab Server Configuration]]
 
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*[[Boyd Drive Setup]]
 
−
*[[Computer for STARS software]] STARS is CMG's fluid modelling software.
 
  
 
|bgcolor="#CCCCCC"|
 
|bgcolor="#CCCCCC"|
 
|valign="top"|
 
|valign="top"|
  
−
===Developer===
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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#Image_Transformation|Image Transformation]]
 +
*[[Image_Registration#Image_Registration|Image Registration]]
 +
*[[Image_Registration#Register_MRI_to_HR-pQCT|Register MRI to HR-pQCT]]
 +
 
 +
[[Image_Registration#Similarity_Registration|'''SimilarityRegistration''']]
 +
*[[Image_Registration#Understand_rotation_parameters| Understand rotation parameters]]
 +
*[[Image_Registration#Set_optimizer_scales| Set optimizer scales]]
  
−
====Lab Software Projects====
+
[[Image_Registration#SkiRegistration|'''skiRegistration''']]
−
----
+
*[[Image_Registration#ITK_Rigid_registration_for_HR-pQCT| ITK Rigid registration for HR-pQCT]]
−
*[[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.
 
  
−
====Platforms====
+
==[[Finite Element Modelling]]==
−
----
+
*[[Finite_Element_Modelling#Scanco_Finite_Element_Modelling| Scanco Finite Element Modelling]]
−
Obtaining, compiling and installing software development tools on various systems.
+
*[[Finite_Element_Modelling#FAIM_Finite_Element_Solver| FAIM Finite Element Solver]]
−
*[[Development on OS-X]]
+
*[[Finite_Element_Modelling#FE_Tutorial| FE Tutorial]]
−
*[[Development for Linux]]
+
*[[Finite_Element_Modelling#Prepare_AIMs_for_FE_Analysis| Prepare AIMs for FE Analysis]]
−
*[[Development on Windows]]
 
−
*[[Development on OpenVMS]]
 
  
−
====Languages and Toolkits====
+
==[[Software Plugins and Codes]]==
 
----
 
----
−
*[[C++ Development]]
+
*[[Software_Plugins_and_Codes#ImageJ| '''ImageJ''']]
−
*[[Creating VTK Classes]]
+
*[[Software_Plugins_and_Codes#Amira| '''Amira''']]
−
*[[ITK Development]]
+
*[[Software_Plugins_and_Codes#R|'''R''']]  
−
*[[Matlab Development]]
+
*[[Software_Plugins_and_Codes#ParaView| '''ParaView''']]
−
*[[Writing plugins for ParaView]]
 
  
−
====Development Tools====
+
==Languages and Toolkits==
−
----
+
*[[C++|'''C++''']]
−
*[[Subversion (SVN)]] for accessing the source code of lab software.
+
*[[VTK|'''VTK''']]
 +
*[[ITK|'''ITK''']]
  
−
===Miscellaneous===
+
==Miscellaneous==
−
----
+
*[[Software_Development_Platforms| '''Software Development Platforms''']]
−
*[[Wireless Network in Morphometrics Lab]]
+
*[[Archive|'''Archive''']]  
−
*[[Archive]] Obsolete stuff here.
 
−
*[[Research Group Contact Info]]
 
  
 
|}
 
|}
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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>

Latest revision as of 19:30, 5 May 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.


The Purpose

It's to facilitate information exchange within the lab and keep up-to-date How To and User Manuals for lab's technical procedures and FAQ.
BonelabScanners.JPG
Read me

  1. Use Ctr+F to search within any page.
  2. Never include login credentials especially password anywhere.
  3. It's all users' responsibility to keep the info precise, updated, abundant, and useful, through editing/addition/deletion as needed by clicking [edit] on the top-right corner of a page or item. This includes combining same/similar topics besides an item whenever appropriate.
  4. Add a redirect line after each new item for consistency:
    Redirect.jpg Return to Contents or Return to Main Page
  5. Click Help on navigation list on the left penal for detailed editing instructions.
  6. Contact Ying if you are not sure where to put a new item or could not find an item.

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
Retrieved from "http://bone.wiki/index.php?title=Main_Page&oldid=7123"