BIOQUANT OSTEO Getting Started Handbook Bioquant... · Author: BIOQUANT Image Analysis Corporation...

Getting Started

Copyright 2014BIOQUANT Image Analysis Corporation

5611 Ohio Avenue, Nashville, TN 37209phone: 800-221-0549 or 615-350-7866

fax: 615-350-7262email: [email protected]

web: www.bioquant.comRevision 14.1.6, 1-31-2014

14.1.6

®

BIOQUANT OSTEO Getting Started Handbook 2 Copyright © 2014

— BIOQUANT OSTEO Getting Started Handbook —

BIOQUANT OSTEO 2014 Installation

Welcome to the BIOQUANT OSTEO image analysis system installation guide. This guide tells how to install the hardware and software and how to make sure the installations are correct.

• Installing the Hardware (page 3)

• Determining if your Hardware Meets Requirements (page 3)

• Installing the BQV Board (page 6)

• Configuring the Required Desktop Settings (page 15)

• Installing Drivers for the Qimaging Camera (page 16)

• Installing the BIOQUANT Program and Resource Files (page 19)

• Installing Drivers for Motorized Stage or Stage Encoders (page 26)

• Installing Adobe Acrobat Reader (page 28)

• View the Release Notes (page 29)

• Opening BIOQUANT OSTEO (page 30)

• How to Proceed (page 34)


Installing the Hardware

The BIOQUANT OSTEO system requires the BQV custom built board.

This section covers determining if your computer meets required specifications, installing the BQV board, setting up the ideal desktop screen resolution, and installing drivers for the optional QImaging Camera.

Note: If your BIOQUANT OSTEO system purchase included a computer from BIOQUANT Image Analysis Corporation, the driver for the BQV board and the BIOQUANT OSTEO software are already installed, and the BQDATA folder has already been created. Skip to “Opening BIOQUANT OSTEO” on page 30.

Topic Contents

• Determining if your Hardware Meets Requirements (page 3)

• Installing the BQV Board (page 6)

• Configuring the Required Desktop Settings (page 15)

• Installing Drivers for the Qimaging Camera (page 16)

Determining if your Hardware Meets Requirements

Before continuing with the BQV installation, confirm that the computer meets required specifications and the Windows 7 Operating System has been installed. If you are using a camera or tracking device, also confirm that it is supported.



Procedure

1. Determine if your computer meets these requirements:

a. Multi-core Intel Processor: e.g., I7 or Xeon processor

Core speeds of 3.5 gHz or higher recommended.

Dell Precision mini-tower computers are recommended (call for us to e-mail you a Dell item list).

b. At least 8 GB RAM

c. Mini-Tower Chassis with room for 1/2 length PCIe board.

The BQ-V imaging board is a half length PCIe board.

d. Support for 1920x1200 desktop resolution required. Dell 24" Ultrasharp monitor recommended.

e. For external video cards, a nVIDIA Quadro series graphics adapter, such as the 600 or higher is required.

If you have integrated video, the Intel I7 3770K processor with integrated HD4000 gpu or better is required.

f. Windows 7 Professional or Enterprise Operating System has been installed.

Supported: Windows 7 64 or 32-bit Professional or Enterprise

Not Supported: Windows Vista 32-bit or 64-bit, Older Windows Versions: Windows XP, Windows 98

2. If using a camera, determine if it is supported:



Recommended Cameras

• QImaging color Aqua EXi, cooled

• QImaging Retiga EXi, cooled or uncooled

Cameras Also Supported

• QImaging color Micropublisher 5.0,cooled or uncooled

• QImaging color QICAM, cooled or uncooled

Legacy Support for Cameras

For existing, backward compatible support (NOT RECOMMENDED because live image size is only 640 x 480):

• Analog RGB video cameras, (NTSC or PAL) such as the Optronics DEI-750 or Sony DCX-390P.

Note: A special cable must be purchased from BIOQUANT for these cameras to connect to the BQV board.

3. If using a tracking device, such as a motorized stage or stage encoders, determine if it is supported:

Supported Tracking Devices

• Motorized Stages: ASI MS2000, MS4000, MS4400, Ludl Bioprecision, Ludl BioPoint 2.

• Stage Encoders: Marzhauser MTM, Boeckeler 2M, Boeckeler 3M stage encoders.



Note

• Variations of stage controllers may not be supported. Call BIOQUANT before purchasing a tracking device to insure compatibility.

• If you did not purchase the motorized stage or stage encoders from BIOQUANT there is a one time fee for purchasing the BIOQUANT driver for these devices. Contact BIOQUANT for a quotation.

4. Continue with Installing the BQV Board (page 6).

Installing the BQV Board

This procedure walks you through installing the BQV board on a Dell Precision mini-tower computer. If you do not have the recommended Dell computer, try installing the BQV using this procedure. If you need assistance, feel free to contact Technical Support at 800-221-0549 Extension 11.

Topic Contents

• Part One: Physically Inserting the BQV Board (page 6)

• Part Two: Installing the BQV Board’s Driver (page 8)

Part One: Physically Inserting the BQV Board

1. On the mini-tower case, pull the release latch on the top of the case.

This causes the side of the case to open.



2. Remove the case side to reveal the mother board.

3. Lay the computer on its side (with the mother board side down).

4. Tap the metal frame of the computer with your hand.

This discharges any static electrical build-up. Static electricity can damage computer components.

5. Inside the computer, release the blue retention clips to release the latch that holds the computer cards in place.

6. Depending on your BQ-V board type, look inside and locate the PCI or PCIe slots in the computer.

Your BQ-V board may be a PCI or a PCIe board.

PCIe slots come in different sizes. All sizes are compatible with the BQ-V (PCie) board.

7. On the computer frame, if there is a cover over the opening for the board’s connection ports, remove it.

8. Remove the BQV board from its anti-static wrap.

9. Line the board’s teeth up with the chosen PCIe slot and push it into place.

The board will fit snugly and evenly. A gentle snap may be heard as the board pops into place.

10.Check to see if the BQV board is seated evenly in the PCIe slot.

If it is, the gold teeth will be hidden inside the slot and the green edge of the board will be parallel to the top of the slot. There should be no rocking movement.



11.Secure the board with the latch so that the blue clips are back in their original position.

12.Replace the computer side, securing the latch at the top of the computer.

13.If the computer is on its side, turn it back upright.

14.Continue with “Part Two: Installing the BQV Board’s Driver” on page 8.

Part Two: Installing the BQV Board’s Driver

Windows 7: Installing the BQV Board Driver

Use this procedure to install the BQV board driver on the Windows 7 64 or 32-bit operating system.

1. Turn the computer on.



2. From the Start bar menu, choose Control Panel.

Figure —Start Bar with Control Panel box

3. On Control Panel, click “Hardware and Sound.”



Figure —Hardware and Sound box

On Hardware and Sound you will click Device Manager under Devices and Printers.

4. On Hardware and Sound, under Devices and Printers, click “Device Manager.”

5. On Device Manager, under Other Devices, click Multimedia Video Controller.



Figure —Device Manager

Click “Multimedia Video Controller.”

6. From the Action menu, choose Update Driver Software.



7. From the “How do you want to search for driver software?” box, choose “Browse my computer for driver software.”

Figure —Update Driver Software - BQV Box

8. On the “Browse for driver software on your computer” box:

a. Insert the BIOQUANT OSTEO DVD into the DVD drive.

b. Click the Browse button to open “Browse for folder.”



c. On the Browse for folder box, navigate to the OSTEO DVD drive. Then click the triangle icon to expand the “BQ-V Driver” folder. Then click to highlight one of the following, based on your version of Windows 7:

• BQ-V Driver for Win32

• BQ-V Driver for Win 64

Figure —Browse For Folder box

d. On the Browse for folder box, click OK.

The BQ-V Driver path should now be in the edit box.

9. On “Browse for driver software on your computer”, click Next.



10.On the Windows Security message, click “Install the driver software anyway.”

Figure —Windows Security box

11.On “Windows successfully updated your device driver,” click Close.

Figure —Update Driver Software - BQ-V

12.Close the Device Manager.

13.Close the Control Panel.

14.Continue with “Configuring the Required Desktop Settings” on page 15.



Configuring the Required Desktop Settings

BIOQUANT OSTEO is designed to work with a wide screen 24” monitor.

This procedure walks you through setting the desktop resolution to the required 1920 x 1200.

It also sets the Theme to the BIOQUANT Windows 7 Theme. This theme sets the border padding to 0, the ideal setting for BIOQUANT windows and boxes. You are welcome to change the background image after the theme is installed, as long as you don’t choose a different theme.

Windows 7: Configuring the Desktop Settings

1. Right click on the Windows 7 desktop to open a menu.

2. From the menu, choose Screen Resolution.

3. From the Resolution drop list, choose 1920 x 1200.

Figure —Change the appearance of your display box

4. Click the OK button.



5. Insert the BIOQUANT OSTEO DVD.

6. On the Windows menu that opens, choose “Open Folder to View Files.”

At this point DO NOT click Run Setup.exe.

7. On the OSTEO DVD, navigate to the BIOQUANT Windows 7 Theme folder.

8. In the BIOQUANT Windows 7 Theme folder, double click the file BIOQUANT-Windows7-Theme.themepack.

The Personalization box opens and the theme is set.

9. Close the Personalization box.

10.Choose from the following:

• If you have purchased a supported QImaging camera, continue with “Installing Drivers for the Qimaging Camera” on page 16.

• Otherwise continue with “Installing the BIOQUANT Program and Resource Files” on page 19.

Installing Drivers for the Qimaging Camera

BIOQUANT OSTEO has integrated support for the following QImaging color digital cameras: Aqua color digital camera, Retiga EXi color digital camera, QICAM-F color digital camera, MicroPublisher 5.0 color digital camera.



Notes

• If you have purchased a computer from BIOQUANT, as well as a QImaging camera, the drivers have already been installed. Skip to “Opening BIOQUANT OSTEO” on page 30.

• Before purchasing a QImaging camera from another vendor, contact our sales department to ensure that it is a compatible model. The QImaging camera require a Firewire board with an internal power connector that connects from the Firewire board to the power supply.

• Windows 7 64-bit only supports the PCIe version of the Firewire card that comes with supported QImaging cameras.

If you are moving a supported QImaging camera over from a previous Windows 32-bit installation and you are now using Windows 7 64-bit, then you will need to upgrade the firewire card from PCI to PCIe.

QImaging cameras require a special firewire card with an internal power connector.

Contact BIOQUANT Technical Services for more information.

Procedure

1. If you are moving the QImaging Camera from a previous BIOQUANT machine:

• Remove the Firewire board that originally came with the QImaging Retiga camera from the original BIOQUANT computer. This is a special firewire card that has an internal power connector. If connected, disconnect the internal power connector before removing the board.



• Windows 7 64-bit Note: If your previous installation was under a 32-bit version of Windows, you will need to upgrade your firewire card to the PCIe version. Contact Technical Services for more information.

2. Shut down your new computer and remove the case.

3. Insert the Firewire board into an empty PCI (Windows 32-bit only) or PCIe slot (Windows 32-bit or 64-bit) depending on your Firewire board type.

4. Connect the internal power connector to the power input on the board.

5. Replace the case on the computer. DO NOT connect the Firewire cable to the camera yet.

6. Restart the new computer.

7. Insert the BIOQUANT OSTEO Installation DVD into the DVD drive.



9. On the OSTEO DVD, navigate to the QImaging folder.



10.On the OSTEO DVD, in the QImaging folder, there are two installation files, one for 32-bit Windows 7 and one for 64-bit Windows 7. Right click on the file that matches your version of Windows 7 and choose Run as Administrator to install the QCapture software. Follow the installation instructions.

As of the OSTEO 2014 release, the current QCapture software version is 2.0.13.1.

QImaging Files:

32-bit file: QCamInstaller-2-0-13-1-32bit.exe

64-bit file: QCamInstaller-2-0-13-1-64bit.exe

11.Reboot the Computer.

12.Plug the QImaging camera into the Firewire board using the Firewire cable (see Hardware Diagram).

13.Turn on the QImaging camera using the switch on the top of the camera.

14.Continue with “Installing the BIOQUANT Program and Resource Files” on page 19.

Installing the BIOQUANT Program and Resource Files

This section covers installing the BIOQUANT OSTEO 2014 program and resource files. The resource files include the BIOQUANT Manuals, Sample Datasets and Images.

Note: Before the BIOQUANT Software is installed make sure that all the Hardware has been installed and configured correctly. See “Installing the Hardware” on page 3.



Procedure

If the Auto Insert functionality is implemented on your computer, the BIOQUANT OSTEO installation screen will open when the DVD is put into the DVD drive. If it does not, do the following to open it.

1. Put the BIOQUANT OSTEO DVD in the computer’s DVD drive.

If an “AutoPlay” box opens, under “Install or run program” choose “Run Setup.exe.”

The BIOQUANT OSTEO 2014 installation program opens.

Figure —BIOQUANT OSTEO 2014 Setup box

2. On the Welcome box, click the Next button.



3. On the Accept or Decline the Software License Agreement box, do the following:

Figure —Accept or Decline the Software License Agreement box

a. Fill in the requested information.

b. After reading, signing and returning to BIOQUANT the license agreement found in your black folder, choose “I accept the software license agreement.” Then click the OK button.

To abort the installation, click the button next to, “I do not accept the software license agreement,” and click the OK or Cancel button.



4. On the Installation Folder box, choose from the following:

Figure —Choose Location

• The default BIOQUANT OSTEO directory is C:\BQOSTEO2014. To install to this directory, on the Installation Folder box click Next. On the Ask Permission message, click Yes.

• To install to a different directory:

i. Click the Change button.

ii. On the Browse for Folder box, navigate to a new destination directory.

iii.To create a new folder, click the Make New Folder button.

iv. Type in a new name for the folder.

v. Click the OK button to close the Browse for Folder box.

vi.Then on the Installation Folder box, click Next.

vii.On the Ask Permission message, click Yes.



5. On the Ready to Install box, confirm the installation settings before the installation of BIOQUANT OSTEO. If the installation setting are not correct, click the Back button and update them. If the installation settings are correct, click the Next button.

The BIOQUANT OSTEO software installs.

6. On the Resource Installation box, to install Sample Datasets, Images, and Manuals, click the Install button.

Clicking the Next button before you click the Install button will complete the OSTEO 2014 software installation without installing the Sample Datasets, Images, and Manuals.

To access the resource files for Sample Data Sets, Sample Images, and Manuals at a later point, on the OSTEO 2014 DVD navigate to the Resource folder. In the Resource folder, double click the Setup.exe file to perform the support files installation.

Figure —Resource Installation box

Click on the Install button to install BIOQUANT’s support files



7. On the Select Packages box, choose the support files you would like to install. By default, all boxes are selected. When done, click Next.

Figure —Choose Support Files to Install

8. On the Ready to Install box, click Next to begin the installation of the resource files.

If any of the installation settings are inaccurate, click the Back button and adjust the settings.

Figure —Confirm Installation Settings

Click Next to begin installation.



The sample Data sets install in a subdirectory called BQ2014 off of the BQDATA directory, for example, C:\BQDATA\BQ2014

The manuals install in a subdirectory called Manuals off of the BIOQUANT OSTEO directory, for example, C:\BQOSTEO2014\Manuals.

The sample images install in a subdirectory called Sample Images off of the BIOQUANT OSTEO Images directory, for example, C:\BQOSTEO2014\Images\Sample Images.

The Setup status bar appears while the BIOQUANT files are copied to the computer’s hard drive.

9. On Installation Successful box, click Finish to exit the completed installation.

Figure —Complete Installation



10.When finished with installation, the Notice box will state, “Your computer must be rebooted...” Click Yes.

Figure —Notice

11.Choose from the following to continue:

• If you have a tracking device, such as a motorized stage or stage encoders, continue with “Installing Drivers for Motorized Stage or Stage Encoders” on page 26.

• If you do not have a tracking device, and the Adobe Acrobat Reader has not been installed on this computer, continue with “Installing Adobe Acrobat Reader” on page 28.

The Adobe Acrobat Reader is required to view the BIOQUANT OSTEO Manuals.

• If you do not have a tracking device and the Adobe Acrobat Reader has been installed on this computer, continue with “View the Release Notes” on page 29.

Installing Drivers for Motorized Stage or Stage Encoders

BIOQUANT OSTEO supports the following motorized stages: ASI MS2000, MS4000, MS4400, Ludl Bioprecision, Ludl BioPoint 2. BIOQUANT OSTEO supports the following stage encoders: Marzhauser MTM, Boeckeler 2M, Boeckeler 3M stage encoders. Variations of stage controllers may not be supported. Call BIOQUANT before purchasing a tracking device to insure compatibility.



Notes

• If you have purchased a computer from BIOQUANT, as well as a motorized stage or stage encoders, the drivers have already been installed.

• If you did not purchase the motorized stage or stage encoders from BIOQUANT there is a one time fee for purchasing the BIOQUANT driver for these devices. Check with sales prior to purchasing a tracking device to insure that the model is compatible with BIOQUANT.

Procedure

1. Insert the BIOQUANT OSTEO DVD into the computer.



3. On the OSTEO DVD, navigate to the Stage Statement folder.

4. Right click on the bqstage.ini file and choose Copy.

5. Close the OSTEO DVD window.

6. On the Windows 7 desktop, right click the BIOQUANT OSTEO program icon to open a menu.

7. Choose Open File Location to open the C:\BQOSTEO2014\Program folder.

8. From the Organize menu, choose Paste.

Alternatively, right click in the Program folder area and choose Paste from the menu.



9. Close the Program folder window.

10.Connect the 9 pin serial cable from the Serial IN (ASI) or RS232 or COM (Marzhauser) port on the stage controller to the COM1 port on the Computer.

11.Turn the stage controller ON.

12.Choose from the following to continue:

• If the Adobe Acrobat Reader has not been installed on this computer, continue with “Installing Adobe Acrobat Reader” on page 28.

• If the Adobe Acrobat Reader has already been installed, continue with “View the Release Notes” on page 29.

The Adobe Acrobat Reader is required to view the BIOQUANT Manuals

Installing Adobe Acrobat Reader

BIOQUANT OSTEO contains documentation in the form of Help Files and PDF Manuals. To view the PDF Manuals, the system must have a copy of the free Adobe Acrobat Reader installed. The latest copy of the Adobe Acrobat Reader installation that was available at the time of making the OSTEO DVD is provided. You are also welcome to install the latest free version by downloading it from Adobe’s website (www.adobe.com).

Procedure




2. On the BIOQUANT OSTEO DVD, double click to open the Acrobat folder, then click “Install Acrobat Reader.exe.”

The version of Adobe Acrobat Reader included at the time of the BIOQUANT OSTEO 2014 release is Acrobat Reader X.

3. The Adobe Reader installation program opens. Follow the directions in the installation program to install.

4. Continue with “View the Release Notes” on page 29.

It is recommended that you read the BIOQUANT OSTEO 2014 Release Notes before using the software.

View the Release Notes

The Release Notes for BIOQUANT OSTEO 2014, v14.1.6, 1-31-2014, are found on the root of the BIOQUANT OSTEO 2014 DVD in PDF format. It is recommended that you read the BIOQUANT OSTEO 2014 Release Notes before using the software.

Procedure






3. On the OSTEO DVD, double click the BIOQUANT OSTEO Release Notes.pdf.

Figure —BIOQUANT OSTEO Release Notes.pdf

4. Continue with “Opening BIOQUANT OSTEO” on page 30.

Opening BIOQUANT OSTEO

The BIOQUANT OSTEO software and the BQV Board have been properly installed when the BIOQUANT program can be opened.



Procedure

1. Confirm the following:

• You have installed the BQV Board and its drivers.

See “Installing the BQV Board” on page 6.

• You have set the desktop resolution to 1920 x 1200.

See “Configuring the Required Desktop Settings” on page 15.

• If you have a supported QImaging camera, you have installed its drivers.

See “Installing Drivers for the Qimaging Camera” on page 16.

• If you have a supported tracking device, you have installed its drivers.

See “Installing Drivers for Motorized Stage or Stage Encoders” on page 26.

• You have installed the BIOQUANT OSTEO program and its resource files.

See “Installing the BIOQUANT Program and Resource Files” on page 19.

2. If you have a supported QImaging camera, make sure the camera is currently ON.



3. Open the BIOQUANT system by double-clicking the BIOQUANT OSTEO icon on the desktop (or in the BIOQUANT folder on the desktop).

Figure —BIOQUANT OSTEO icon

BIOQUANT OSTEO opens. If BIOQUANT OSTEO does not open or if you get an error message, first make sure that you have inserted the BQV Board, installed the BQV Board’s driver, and configured the desktop settings correctly, see “Installing the Hardware” on page 3. If you still experience problems opening the BQ-OSTEO software, contact technical support (1-800-221-0549 Ext 1 or 1-615-350-7866 Ext 1 or [email protected]).

4. If you have installed drivers for a supported QImaging camera, do the following:

a. In BIOQUANT, from the Image menu, choose Open QImaging Camera.

A live image from the camera should appear in the Image window.

b. In the Image region (Live Image Type), click Auto Exposure.

c. In the Image region (Live Image Type), click White Balance.

d. For more information on setup for the QImaging cameras, see the BIOQUANT OSTEO Manual, Image Region and Image Menu chapter, Using the QImaging Camera procedure.

5. If you have a legacy analog camera, do the following:



a. Make sure you have plugged the purchased BIOQUANT cable into the camera on one end and the BQV board on the other end. Then turn the analog camera ON.

b. In BIOQUANT, from the Image menu, choose Open Analog Camera.

c. If you do not get a live image or if the live image looks weird, from the Image menu choose Camera Setup.

d. On Camera Setup, in the Video Signal Type region, choose RGB, Composite, or SVideo depending on your camera signal type.

For Sony DXC-390, choose RGB if you are using the 9 M-44M cable.

If your camera is using a 1 BNC-44M cable, choose Composite.

e. On Camera Setup, in the Video Standard Type region, choose NTSC or PAL, depending on your camera standard.

For most BIOQUANT legacy cameras choose NTSC. For the Sony DXC-390P, choose PAL.

f. For more information on setup for the QImaging cameras, see the BIOQUANT OSTEO Manual, Image Region and Image Menu chapter, Using the Analog Camera procedure.

6. If you have a motorized stage or stage encoders, from the Topo menu, click to check Stage.

The Image window title bar should say “Stage is On.” If it does not, make sure you have followed the procedure “Installing Drivers for Motorized Stage or Stage Encoders” on page 26. If the stage still does not turn on, contact Technical Support (800-221-0549 Ext 11 or [email protected]).



7. Continue with “How to Proceed” on page 34.

How to Proceed

Once the BIOQUANT OSTEO software and BQV have been properly installed, as well as any additional hardware, such as a QImaging camera or a tracking device, the next step is to become familiar with the system.

Topic Contents

• Learn About BIOQUANT (page 34)

• Get an Image (page 35)

• Calibrate the System (page 35)

• Follow a Measurement Protocol (page 36)

Learn About BIOQUANT

Use the following guides to learn more about BIOQUANT.

• In the Guides region, read the pre-loaded “Welcome” guide.

Welcome

This is the first guide that opens when you open BIOQUANT.



• Then in the Guides region, click the Open button and choose “Introduction to BIOQUANT.” Follow this guide to become familiar with the BIOQUANT interface.

Introduction to BIOQUANT OSTEO

This guide will introduce you to basic parts of the software and get you pointed in the right direction for your project.

Get an Image

Open a sample image or get a sample image from the camera. The following guides might be helpful.

In the Guides region, click the Open button and choose from the following:

• Image - Get an Image From the Microscope

This guide walks you through getting a live image from the QImaging Retiga EXi Camera connected to your microscope.

• Image - Open a Scanned or Stitched Image

This guide walks you through opening a large scanned or montaged image of a section.

• Image - Open a Series of Images

This guide walks you through opening a series of images in the BIOQUANT Imaging Toolkit. The BIOQUANT Imaging Toolkit is part of the optional BIOQUANT Imaging Extensions.

Calibrate the System

Before accurate measurements can be taken, the BIOQUANT OSTEO software needs to be calibrated for the Imaging source. To calibrate, do the following:



1. On your desktop, open the file, “BIOQUANT OSTEO Manual.pdf.”

The PDF manuals were part of the Resource file installation. See “On the Resource Installation box, to install Sample Datasets, Images, and Manuals, click the Install button.” on page 23.

If the desktop icon was deleted, click the Windows 7 Start button, then choose All Programs, then choose BIOQUANT OSTEO 2014 v14.1.6, then choose BIOQUANT OSTEO Manual.pdf.

The default directory for the manuals is C:\BQOSTEO2014\Manuals.

2. Use the Bookmarks to navigate to the Section entitled, “Image Region and Image Menu.”

3. Under “Image Region and Image Menu,” choose “Calibration.”

4. Under “Calibration,” choose from the following:

• Calibrate a Camera on a Microscope

• Calibrate a Digital Scan

• Calibrate for a Sequence of Images

Follow a Measurement Protocol

Choose from the following:



Read the OSTEO Manual

1. On your desktop, open the file, ”BIOQUANT OSTEO Manual.pdf.”

The PDF manuals were part of the Resource file installation. See “On the Resource Installation box, to install Sample Datasets, Images, and Manuals, click the Install button.” on page 23.

If the desktop icon was deleted, click the Windows 7 Start button, then choose All Programs, then choose BIOQUANT OSTEO 2014 v14.1.6, then choose BIOQUANT OSTEO Manual.pdf.

The default directory for the manuals is C:\BQOSTEO2014\Manuals.

2. In the Bookmarks list on the left, choose from the following:

• Click “Prepare for a Study” to learn how to start a BIOQUANT Study.

• Click “Image Region and Image Menu” to learn how to import images, capture images using the camera, use the Imaging Toolkit, use the MicroCT Navigator, and use BIOQUANT Scan.

• Click “Bone Morphometry Measurement Protocols” for the following complete protocols:

• Rodent Trabecular Bone Complete Protocol

• Human Trabecular Bone Complete Protocol

• Basic Cortical Bone Protocol

• Complete Cortical Bone Protocol



• Arthritis Protocol

• Metastasis Protocol

• Osseointegration Protocol

• Chondrocyte Proliferation Protocol

• Strut Analysis Protocol

Follow a Sample Guide

Follow some of the Sample Guides on the Guides Quick list that start with “Measure.” In the Guides region, if you click the Open button, a drop list with these guides opens.

• Measure - Bone Arthritis

This guide walks you through measuring Arthritis indices using sample dataset based on the OSTEO 2014 Template Volume :: Bone Arthritis template.

• Measure - Bone Metastasis

This guide walks you through measuring Metastasis indices using a sample dataset based on the OSTEO 2014 Template Volume :: Bone Metastasis template.

• Measure - Bone Stereology - Referent Data

This guide demonstrates the use of stereology to measure TV, BV, BS, and trabecular geometry referent data using the Merz grid. This guide requires the optional Imaging Extensions for BIOQUANT OSTEO.



• Measure - Chondrocyte Proliferation

This guide walks you through measuring Chondrocyte Proliferation indices using a sample dataset based on the OSTEO 2014 Template Volume :: Chondrocyte template.

• Measure - microCT

This guide helps you learn to measure trabecular structure and trabecular mineralization in microCT data. That includes Tissue Volume, Bone Surface, and Bone Volume, trabecular structure indices, and trabecular optical density. This guide requires the optional Imaging Extensions for BIOQUANT OSTEO.

• Measure - Osseointegration

This guide collects bone structure and contact surface data from dental and orthopaedic implants. It uses a sample data set based on the OSTEO 2014 Template Volume :: Osseointegration template.

• Measure - Tb.Human -Tri TBlue Fl - 1. Trichrome Data

This set of three guides uses a sample dataset based on the OSTEO 2014 Template Volume :: Tb.Human -Tri TBlue Fl Template. This guide covers measuring Tissue Volume (TV), Bone Surface (BS), Bone Volume (BV). These are the basic values used to normalize histomorphometry data across animals.

• Measure - Tb.Human -Tri TBlue Fl - 2. TBlue Data

This guide helps you learn to collect histomorphometry data associated with Wall Width, Ob, and Oc indices. We recommend you finish the “Measure - Tb.Human -Tri TBlue Fl - 1. Trichrome Data” guide before working on this guide.



• Measure - Tb.Human -Tri TBlue Fl - 3. Fluorescent Data

This guide helps you learn to collect histomorphometry data associated with bone formation rate. We recommend you finish the other “Measure - Tb.Human -Tri TBlue Fl - 2. TBlue Data” guide before working on this guide.

• Measure - Tb.Rodent -Tri TRAP Fl - 1. Trichrome Data

This three guide set covers a trabecular rodent study with a trichrome, TRAP, and fluorescent stained slide set. It uses a sample data set based on the OSTEO 2014 Template Volume :: Tb.Rodent -Tri TRAP Fl template. In this first guide, you learn to measure Tissue Volume (TV), Bone Surface (BS), Bone Volume (BV), Adipocyte Volume (Ad.V), as well as collect osteoblast data on the trichrome slide.

• Measure - Tb.Rodent -Tri TRAP Fl - 2. TRAP Data

This guide continues with the TRAP slide in a trabecular rodent Trichrome, TRAP, Fluorescent slide set. You learn to collect histomorphometry data associated with osteoclasts. We recommend you finish the “Measure - Tb.Rodent -Tri TRAP Fl - 1. Trichrome Data” guide before working on this guide.

• Measure - Tb.Rodent -Tri TRAP Fl - 3. Fluorescent Data

This guide continues with the fluorescent slide in a trabecular rodent Trichrome, TRAP, Fluorescent slide set. You learn to collect histomorphometry data associated with bone formation rate. We recommend you finish the “Measure - Tb.Rodent -Tri TRAP Fl - 2. TRAP Data” guide before working on this guide.



• Measure - Tb.Rodent -VK TBlue TRAP Fl - 1. Von Kossa Data

This four guide set covers a trabecular rodent study with a von kossa, toluidine blue, TRAP, and fluorescent stained slide set. It uses a sample data set based on the OSTEO 2014 Template Volume :: Tb.Rodent -VK TBlue TRAP Fl template. In this first guide, you learn to measure Tissue Volume (TV), Bone Surface (BS), Bone Volume (BV), and Adipocyte Volume (Ad.V).

Note: Osteoid measurements are much easier on trichrome sections, so if your lab has a choice, we recommend using the Trichrome, TRAP, Fluorescent serial section set instead.

• Measure - Tb.Rodent -VK TBlue TRAP Fl - 2. TBlue Data

This guide continues with the toluidine blue slide in a von kossa, toluidine blue, TRAP, and fluorescent stained slide set. You learn to collect histomorphometry data associated with osteoblasts. We recommend you finish the “Measure - Tb.Rodent -VK TBlue TRAP Fl - 1. Von Kossa Data” guide before working on this guide.

• Measure - Tb.Rodent -VK TBlue TRAP Fl - 3. TRAP Data

This guide continues with the TRAP slide in a von kossa, toluidine blue, TRAP, and fluorescent stained slide set. You learn to collect histomorphometry data associated with osteoclasts. We recommend you finish the “Measure - Tb.Rodent -VK TBlue TRAP Fl - 2. TBlue Data” guide before working on this guide.

• Measure - Tb.Rodent -VK TBlue TRAP Fl - 4. Fluorescent Data

This guide continues with the fluorescent slide in a von kossa, toluidine blue, TRAP, and fluorescent stained slide



set. You learn to collect histomorphometry data associated with bone formation rate. We recommend you finish the “Measure - Tb.Rodent -VK TBlue TRAP Fl - 3. TRAP Data” guide before working on this guide.

Read the Help Files

From the Help menu, choose Contents to open BQ OSTEO Help. On the Contents tab, choose from the following:

The OSTEO Help Files contain all the content of the BIOQUANT OSTEO Manual. Choose the format that is easiest for you to follow.

• Click “Prepare for a Study” to learn how to start a BIOQUANT Study.

• Click “Image Region and Image Menu” to learn how to import images, capture images using the camera, use the Imaging Toolkit, use the microCT Navigator, and use BIOQUANT Scan.

• Click “Bone Morphometry Measurement Protocols” for the following complete protocols:

Rodent Trabecular Bone Complete Protocol

Human Trabecular Bone Complete Protocol

Basic Cortical Bone Protocols

Complete Cortical Bone Protocols

Arthritis Protocol

Metastasis Protocol

Chondrocyte Proliferation Protocol

Strut Analysis Protocol



• Click the ? button on each region from left to right to learn more about that region.

Acknowledgment

The PDF icon used in the BIOQUANT Documentation is courtesy of http://www.iconfinder.net.


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