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TECHNOLOGYthink forward

User Manual

Bruker AXS

PILOT Release 2008

Part Number: M86-E03065

Publication Date: 14 May 2008

XRD


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PILOT User Manual

Bruker AXS Inc.

5465 East Cheryl Parkway

Madison, WI 53711-5373 USA

Phone +1 (800) 234-XRAY [9729]

Fax +1 (608) 276-3006

E-mail: [email protected] www.bruker-axs.com

Bruker BioSciences

40 Manning Road

Billerica, MA USA

Phone +1 (978) 663-3660

Fax: +1 (978) 667-5993

E-mail: [email protected] www.bruker-biosciences.com

This document covers the PILOT software program.

References to this document should be shown as M86-Exx065 PILOT User Manual.

© 2008 Bruker AXS Inc., 5465 East Cheryl Parkway, Madison, WI 53711. All world rights reserved.

Notice

The information in this publication is provided for reference only. All information contained in this publication is believed to be cor-rect and complete. Bruker AXS Inc. shall not be liable for errors contained herein, nor for incidental or consequential damages inconjunction with the furnishing, performance, or use of this material. All product specifications, as well as the information con-tained in this publication, are subject to change without notice.

This publication may contain or reference information and products protected by copyrights or patents and does not convey anylicense under the patent rights of Bruker AXS Inc. nor the rights of others. Bruker AXS Inc. does not assume any liabilities arisingout of any infringements of patents or other rights of third parties. Bruker AXS Inc. makes no warranty of any kind with regard to

this material, including but not limited to the implied warranties of merchantability and fitness for a particular purpose.No part of this publication may be stored in a retrieval system, transmitted, or reproduced in any way, including but not limited tophotocopy, photography, magnetic, or other record without prior written permission of Bruker AXS Inc.

Address comments to: Technical Publications DepartmentBruker AXS Inc.5465 East Cheryl ParkwayMadison, Wisconsin 53711-5373USA

All trademarks and registered trademarks are the sole property of their respective owners.

Printed in the U.S.A.

Revision History

Revision Date Changes

0 October 2004 Original release.

1 January 2006 Revised and expanded for PILOT Version 2.

2 01 February 2008 Revised and expanded for PILOT Version 2.3.

3 14 May 2008 Revised and expanded for PILOT Release 2008.x-x.


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M86-E03065 iii

Table of Contents

1 About This User Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

1.1 PILOT Features . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

1.2 The Structure of this User Manual. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-1

1.3 Terms and Conventions Used in thi s User Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-2

1.3.1 Typographical Conventions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-21.3.2 Equivalent Terms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-21.3.3 Warnings, Cautions, and Notes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

1.4 Referenced Documentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-3

1.5 X-ray Safety . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

1.6 PILOT Help and Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-4

1.6.1 The “What’s This?” Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-41.6.2 Technical Support . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-5

2 PILOT Suite Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12.1 Introduct ion to Client and Server Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.1.1 Client and Server Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-12.1.2 Client and Server Hardware. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1

2.2 Server Funct ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

2.2.1 Bruker Instrument Service (BIS). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-4

2.3 Client Functions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5

2.3.1 PILOT: Online or Offline Mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-52.3.2 BCP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5

2.4 The Sample Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-72.4.1 Sample Database Benefits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-72.4.2 Structure of the Sample Database . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-82.4.3 Sample Visibility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-82.4.4 Types of Users . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-82.4.5 Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-8

2.5 Access to BCP and PILOT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9

2.6 License Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-9


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3 PILOT Startup and Shutdown . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.1 Starting PILOT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-1

3.1.1 Start BIS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-13.1.2 Start PILOT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-2

3.2 Shutting Down PILOT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

3.2.1 Shut Down PILOT . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-43.2.2 Shut Down BIS. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3-4

4 PILOT User Interface Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-1

4.1 The Interface and Invalid User Input . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

4.2 Title Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-2

4.3 Menu Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-3

4.4 Task Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-5

4.4.1 Program Shortcuts in the Task Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-64.4.2 Stack Bar and Tree View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-7

4.5 Tool Icon Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-8

4.5.1 Image Controls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-94.5.2 Floating Toolbars and the Line Up Command . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-94.5.3 Tool Icon Bar Keyboard Shortcuts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-9

4.6 Task Display Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10

4.7 Image Information Area . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4-10

5 Working With Samples, Trays, and Experiments . . . . . . . . . . . . . . . . . . . . 5-1

5.1 Creating Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-1

5.2 Creating Trays for Screening. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

5.2.1 Individual Trays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-25.2.2 Tray Templates . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-2

5.3 Closing and Saving Samples. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4

5.4 Deleting Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-4

5.5 Archiv ing Samples . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-5

5.5.1 Archiving to .ZIP Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-6

5.5.2 Archiving to CD-ROM. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-75.6 Restori ng Samples from Archives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-8

5.6.1 Restoring Samples from .ZIP File Archives . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-85.6.2 Restoring Samples from CD-ROM Archives . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-9

5.7 Working wi th Experiments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11

5.7.1 Experiments Viewer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5-11


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6 Working wi th Frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-1

6.1 Opening and Integrating Frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-2

6.1.1 Opening a Frame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-26.1.2 Opening Multiple Frames as a Composite Image . . . . . . . . . . . . . . . . . . . . . . . . 6-36.1.3 Selecting Parts of the Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-4

6.1.4 Integrating and Saving RAW Files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-7

6.2 Frame Viewing Opt ions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-9

6.2.1 Image Brightness and Contrast Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-96.2.2 Color Options . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-106.2.3 Zooming In on the Image . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-116.2.4 The Flip Image Function. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-12

6.3 Displaying Frame Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-13

6.3.1 The Image Information Area. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-136.3.2 Displaying Frame Names. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-146.3.3 3D View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-15

6.3.4 Pixel Dump. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-166.4 Example: Integrating Single Frames . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6-17

6.5 Example: Merging and Integrating Multip le Frames . . . . . . . . . . . . . . . . . . . . . . . . . 6-18

7 The Instrument Control Module . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

7.1 Instrument Con tro l . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-1

7.1.1 Manual . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-27.1.2 Update/Home . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-47.1.3 Axes Limits. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-5

7.1.4 Axes Speeds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7-7

8 Single Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1

8.1 Collect Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-1

8.1.1 Sample Setup Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-28.1.2 Experiment Editor Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-38.1.3 Monitor Tab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-9

8.2 Tutorial: Collecting a Single Sample. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-12

8.2.1 Create a New Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-128.2.2 Align the Sample . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-12

8.2.3 Set up the Experiment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-138.2.4 Activate and Run the Experiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8-13

9 High Throughput Screening . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

9.1 Collect HTS . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-1

9.1.1 Sample Setup. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-19.1.2 Tray View . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9-2


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1.3 Terms and Conventions Used in this User Manual

Before using this User Manual, it is important to understand the terms and typographical conventionsused. Certain kinds of formatting in the User Manual’s text are used to identify special kinds ofinformation.

1.3.1 Typographical Conventions

Table 1.1 shows typographical conventions used to help you quickly locate and identify information inthis User Manual.

Table 1.1 — Typographical conventions

1.3.2 Equivalent Terms

Frame/Image

In 2-dimensional XRD, the terms “frame” and “image” refer to the same 2-dimensional view of thediffraction pattern.

Greek and Roman Text

This User Manual uses scientific terminology that may be rendered in Greek text. However, this UserManual follows a convention of using Roman text to the greatest extent possible.

Table 1.2 — Greek and Roman text

Convention Usage

boldfaceSoftware interface elements (such as icons, menu items, and but-tons) to be selected as part of the current procedure.

italics New terms and words requiring emphasis.

monospace Information read from or entered into a command prompt.

>

Navigation through a hierarchical menu. For example, “ChooseStart > Programs > Bruker AXS > PILOT” describes navigatingWindows’ menus from Start to Programs to Bruker AXS to PILOT.

[square brackets] Keyboard input.

Greek Roman

2θ 2-Theta

θ1 Theta1

θ2 Theta2

ω Omega

φ Phi

χ Chi

γ Gamma

http://-/?-http://-/?-


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1.3.3 Warnings, Cautions, and Notes

This User Manual contains notices that you must observe to ensure your own personal safety, as wellas to protect the product and connected equipment. These notices are highlighted in the User Manualby a warning triangle and are marked as follows according to the level of danger.

WARNING!The word “WARNING” alerts you to animmediate or potential hazard that can result indeath, severe personal injury, or substantialproperty damage.

CAUTION!

The word “CAUTION” alerts you to a potentialpractice or condition that could result in minorpersonal injury or damage to the product or

property.

NOTE: The word “NOTE” in bold capital lettersdraws your attention to particularlyimportant information on the product orhandling of the product, or to a particularpart of the product documentation.

1.4 Referenced Documentation

Table 1.3 contains a list of documentation referenced in this User Manual. It is recommended to havethis additional documentation available as you work with this User Manual.

Table 1.3 — Referenced documentation

Documentat ion Part Number Title

M85-Exx002 DIFFRACplus EVA User Manual

M86-Exx007 GADDS User Manual

M86-Exx055 Introduction to 2D XRD

M86-Exx084 PILOT Installation Notes

M86-Exx092 User Manager User Manual

M88-Exx086 DIFFRACplus Part 11 Installation and Administration Guide

M88-Exx099 License Manager User Manual

http://-/?-http://-/?-


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1.5 X-ray Safety

WARNING!

X-ray equipment produces potentially harmfulradiation and can be dangerous to anyone in the

equipment’s vicinity unless safety precautionsare completely understood and implemented. Allpersons designated to operate or performmaintenance on this instrument need to be fullytrained on the nature of radiation, X-raygenerating equipment, and radiation safety. Allusers of the X-ray equipment are required toaccurately monitor their exposure to X-rays byproper use of X-ray dosimeters.

For safety issues related to operation and maintenance of your particular X-ray generator,diffractometer, and shield enclosure, please refer to the manufacturer’s operation manuals or to your

Radiation Safety Officer. The user is responsible for compliance with local safety regulations.

1.6 PILOT Help and Technical Support

1.6.1 The “What ’s Th is?” Func tion

Context-based help is available at any time within PILOT by simply clicking the “What’s This?” icon:

Figure 1.1 — “What’s This?” icon

After clicking the icon, click on any window, control, or field within PILOT to obtain detailed help in apop-up window.


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1.6.2 Technical Support

Users are invited to contact Bruker AXS whenever there are problems or questions related to thesystem. Before contacting Bruker AXS, please:

• If there is a software problem, determine the version of the program.

• Record any error messages.

• Determine conditions and steps that recreate the problem.

If the instrument is in North America, contact our North American Service Center:

Table 1.4 — Bruker AXS North American Service Center contact information

If the instrument is outside North America, contact our Karlsruhe Service Center:

Table 1.5 — Bruker AXS Karlsruhe Service Center contact information

Bruker AXS North American Service Center

Address:

Bruker AXS Inc.

Customer Support

5465 East Cheryl Parkway

Madison, WI 53711-5373USA

Toll-free telephone: 1 (800) 234-XRAY [9729]

Direct line: 1 (608) 276-3087

Fax: 1 (608) 276-3015

E-mail: [email protected]

Web: http://www.bruker-axs.com

Bruker AXS Karlsruhe Service Center

Address:

Bruker AXS GmbH

Customer Support

Östliche Rheinbrückenstr. 49

76187 Karlsruhe

Germany

Telephone: +49 (721) 595-8403

XRD Hotline: +49 (721) 595-6288

E-mail: [email protected]

Web: http://www.bruker-axs.de


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2 PILOT Suite Overview

This Chapter presents an outline of the PILOT Suite, including:

• A guide to interrelationships among the Suite’s various programs (and the Suite’srelationships to external programs);

• A discussion of the Sample Database, which manages data collected by PILOT;

• Access levels for programs within the PILOT Suite; and

• Software Licenses for the PILOT Suite.

2.1 Introduction to Cl ient and Server Functions

2.1.1 Cl ient and Server Software

From a software and operational viewpoint, the D8 family of systems use the PILOT Suite to control alloperations from experiment setup to image analysis for a typical X-ray diffraction study.

To accomplish this, the various programs within the PILOT Suite have a client/server relationship(Figure 2.1), in which the server program (BIS, the Bruker Instrument Service) executes commandsgiven by one of several client programs (PILOT or BCP, the Bruker Configuration Program).

2.1.2 Cl ient and Server Hardware

The PILOT Suite typically runs on two computers: a Server and a Client.

The Server computer’s purpose is to communicate with the hardware, allowing the user to control theinstrument. The Server also contains software for aligning the system.

A Client can be any computer that is connected to the Server computer through a TCP/IP network.PILOT runs on the Client and controls the instrument through a connection to BIS, which must berunning on the Server. Most of the diffraction experiment is carried out on the Client.

NOTE: Single-computer installations of the

PILOT Suite are possible. In theseinstallations, all of the software runs on asingle computer (referred to as aServer).

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Figure 2.1 — PILOT hardware and software relationships

Figure 2.2 — PILOT single-computer configuration

PILOTClient Computer:

BIS BCP

Instrument

Server Computer:

Enclosure andgoniometercontroller

Single Computer

On single-computer systems, thisexternal computer runs both BIS andPILOT, combining the functionality ofthe Client and Server.


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Figure 2.3 — PILOT dual-computer configuration

TCP/IPhub

Server Computer

On dual-computer systems, thiscomputer uses BIS and to controlthe instrument. The Server cancarry out experiments while theClient is used for offline processingof data.

Client Computer

On dual-computer systems, thisexternal computer runs PILOT,using experiment information (i.e.,area detector frames) gatheredfrom BIS to analyze the sample.

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2.2 Server Functions

2.2.1 Bruker Instrument Service (BIS)

BIS acts as a server to the client programs PILOT and BCP, providing a link between the hardware andsoftware. Once a connection is established, BIS executes hardware commands sent by the client

programs. BIS can also be used as a service tool, displaying diagnostic messages during operation.

Figure 2.4 — BIS main window


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2.3 Client Functions

2.3.1 PILOT: Online or Off line Mode

The PILOT program is a GUI with multiple plug-ins, or modules, for different aspects of an experiment.PILOT’s Sample Database (Section 2.4) stores relevant data from each step in the experiment. Details

of the functions available in the GUI are explained in detail later in this User Manual.

PILOT can operate in either online or offline mode. In online mode, PILOT is connected to BIS andsends commands to BIS for the purpose of collecting data. In offline mode, PILOT is not connected toBIS and does not require communication with the instrument (for example, when viewing frames thathave already been collected).

In online mode, you must start BIS, PILOT, and optionally, VIDEO. In offline mode, you only need tostart PILOT.

2.3.2 BCP

BCP, the Bruker Configuration Program, is used to configure BIS, as well as to provide instrumentcontrol and alignment tools.

From the BCP menu (see Figure 2.5), default parameters for specific hardware elements can beupdated. BCP writes these values to the file BrukerInstrument.ini, which is read by BIS. When changesare made in BCP, BrukerInstrument.ini is saved (BIS must be restarted to read in the new values).

A variety of hardware functions are available from BCP’s Tools menu. Frequently used features are:

• Dark Current — if you are using a CCD detector, generates dark current files fordifferent exposure times.

• Manual — allows you to drive the goniometer and manually open the shutter; and

• Update and Home — allows you to update the goniometer angles manually and at their

reference settings (D85 goniometers only).• Collision Recovery — allows you to recover from collisions between the instrument’s

axes.

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2.4 The Sample Database

The Sample Database is used for the storage of data generated by the PILOT Suite. It is designed totransparently handle data from all of the PILOT modules without intervention from the user.

The Sample Database is used internally by the PILOT Suite and is not available for user customizationor manipulation. It automatically starts on computer startup, and automatically stops when the computer

is shut down.

2.4.1 Sample Database Benef its

Below are Sample Database benefits from a user perspective. Note that the Sample Database replacesso-called “flat” files (which offer none of the features listed below).

Multi-user Environments

• User management and group management allow sharing and restricting access tosample data.

• Multiple users can access the sample data simultaneously.

• The Sample Database allows access from one or more remote locations (i.e., clientPCs).

• The Sample Database protects sample data as it enforces that:• Only a single user can open a specific sample for write access at a time; and• That each user can only open samples to which they were granted access.

Data Integrity

• The Sample Database guarantees the integrity of all sample data at all times (i.e.,transactions are used to ensure that either all or no changes are committed).

• The Sample Database enables network administrators to use industry-standard tools toefficiently and effectively back up and restore sample data.

Data Sharing

• The Sample Database enables all of an application’s modules to share sample dataseamlessly and transparently. The same is true for sharing data between differentapplications and between different operating systems).

Scalability

• The Sample Database provides fast access to thousands of samples. For example, theuser can easily sort the samples shown in a “Sample Open” type dialog by sample name,user, group, date, etc.

• The Sample Database technology allows applications to grow and satisfy future userrequirements while processing increasingly complex sample data with great ease andspeed.


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2.5 Access to BCP and PILOT

Bruker software allows different user accounts to have different levels of access to the instrument:

• Service

• Security

• Administrator • User

• Non-user

NOTE: You need Bruker InstrumentAdministrator rights to run BCP andBruker Instrument User rights to runPILOT. Typically, your laboratorymanager will already have your useraccount configured or you will be usingthe default accounts as shipped byBruker.

2.6 License Considerations

You need a software license to activate your purchased software packages, options, and/or features.

PILOT requires a valid license file to operate. This file, “bn-license.dat”, must be present in the rootdirectory of drive C:\ for the software to start properly. If the license file is not present or has expired, anerror window will appear when you try to start PILOT (Figure 2.6). This window prompts you to run theLicense Manager application to obtain a valid license for PILOT.

For more information on licenses and License Manager, refer to M88-Exx099 License Manager UserManual.

Figure 2.6 — “No valid license” window

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NOTE: In order to connect to the sampledatabase, the sample database must beaware of each operating system accountthat is allowed to connect to it. If you arelogged into an operating system accountthat the sample database does not

recognize (“PILOT User 1” in thisexample), attempting to log into PILOTwill give the error shown in Figure 3.4.

To correct this problem, refer to theSection “Adding Users to the SampleDatabase” in M86-Exx084 PILOTInstallation Notes.

Figure 3.4 — Login failure: sample database is not aware of operating system account

3. For online operation within PILOT, choose Instrument > Connection. In the “InstrumentConnection” window, enter the instrument host name. The window shows the defaulthost. Click Connect.

Figure 3.5 — Instrument connection dialog

NOTE: By editing the “bn-config.py”configuration file, PILOT may beconfigured to start without displaying theInstrument Connection window. In thismode, PILOT automatically connects toa user-specified IP address or DNSname of a computer running BIS.

You are now ready to begin using PILOT.

NOTE: If BIS is running on the samecomputer as PILOT, use l ocal host

for the host name.

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3.2 Shutting Down PILOT

3.2.1 Shut Down PILOT

1. First, log out of the Sample Database by choosing Sample > Logou t. In the “ClosingSample” window, choose whether to save or discard the changes to the Sample

Database.

Figure 3.6 — “Closing Sample” window

NOTE: The “Closing Sample” window appearseven if no apparent changes were madeto the Sample Database because thedate and time of the last access are heldin the Sample Database and differ fromthe current date and time.

2. Within PILOT, choose Sample > Exit. PILOT closes.

3.2.2 Shut Down BIS

1. To stop BIS, click the Exit button in the upper right-hand corner of the BIS window. Youmay be asked to place the generator into standby mode.

2. You will be asked to confirm that you wish to exit BIS. Click OK. BIS closes.


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4.1 The Interface and Inval id User Input

Throughout the PILOT user interface, a typical user input field does not accept invalid user input. Forexample a number-type input field ignores letters (i.e., the letter is neither displayed nor causes an errormessage or keyboard beep). An integer-type field does not accept a floating point. A field expecting apositive number does not accept a minus sign.

Input fields with a pink background indicate invalid entries. Disabled (i.e., grayed-out) fields indicatethat a feature is not available (i.e., not supported or dependent upon the instrument configuration).

• A number-type user input field is highlighted with a pink background color if a numberentered exceeds a valid range or a valid resolution. For example, a field turns pink if auser enters 1.234 or 123 (and the valid range is 1.00 to 100.00).

• File name-type user input fields only accept characters that are valid in a file name. Thefield is highlighted with a pink background color if the file does not exist (or while the useris typing in the file name).

NOTE: The highlight background color can beconfigured; the default is pink.

4.2 Title Bar

The Title Bar displays the name and version of the software, user name, sample name, license type,and the name of the currently-active module. The right-hand edge of the Title Bar also contains the

three buttons used by Windows for minimizing, restoring, and closing the PILOT window.

NOTE: Throughout the PILOT user interface,input fields with a pink background

indicate invalid entries. Disabled(grayed-out) fields indicate that a featureis not available (i.e., not supported ordependent upon the instrumentconfiguration).


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4.3 Menu Bar

The Menu Bar provides drop-down menus for a variety of file operations, image tools, and help files.

An icon for the currently-active window appears on the left side of the Menu Bar. Clicking on this iconwill allow you to minimize, restore, resize, close, or move the currently-active window.

NOTE: In 21 CFR Part 11 installations, themenu item 21CFR11 appears. It allowsyou to sign electronic records andchange your password (Appendix B).

NOTE: When the Collect HTS module is active,the menu item Screening appears. Itallows you to import tray information(Section 9.1.4).

Table 4.1 — Sample menu items

Sample Menu

Login...Opens a dialog window for logging into theSample Database using your username andpassword.

Logout Logs out of the Sample Database.

ChangePassword...

Opens a dialog for changing the currentuser’s password.

NewLets you create a new Sample, Tray, or TrayTemplate.

Open Opens a previously saved Sample or Tray.

Save Saves the current sample.

Close Closes the current sample.

ArchiveLets you archive you current sample, or man-age your archived samples.

Notes...Opens a Sample Notes window for the cur-rent sample.

ExportLets you export your sample data as an XMLfile.

Exit

Exits the application. This menu item has the

same function as the button in the cornerof the Title Bar.

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Table 4.2 — Instrument menu items

Table 4.3 — Windows menu items

Table 4.4 — Help menu items

Instrument Menu

Connect...Opens a connection to a host computer run-ning BIS.

DisconnectIf connected already, choose this commandto disconnect.

Show Status...Opens a window showing a summary of thecurrent status of the instrument and yourconnection to it.

Toggle Shutter

Instructs BIS to send a shutter open or closecommand to the instrument. If all hardwareinterlocks and safety circuits are satisfied,the shutter will open and close.

Abort... Stops a currently-running data set.

Windows Menu

WindowSelection

Displays a list of active windows. Any ofthese windows may be made active by click-ing its title in the Window Selection menu.

Help Menu

ManualOpens an electronic copy of the PILOT UserManual in .pdf format.

About PILOT...Displays version and copyright informationfor PILOT.


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4.4 Task Bar

The Task Bar allows you to choose one of PILOT’s four overall categories of functionality:

• SIngle Sample

• High Throughput Screening

• Texture• Instrument

For more information on individual menus, see the menus’ corresponding chapters in this Manual.

NOTE: If the Task Bar is not visible, there is noopen sample. Open a sample by clickingSample > Open > Sample or Tray (depending on your application), orcreate a new sample or tray by clickingSample > New > Sample or Tray.

Icon Task Description

Single Sample

Collect Sample Set up a single sample and collect data.

XRD2 Eval Display and integrate single and multiple frames.

High Throughput Screening

Collect HTS Set up a tray and col lect data.

XRD2 Eval Display and integrate single and multiple frames.


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Table 4.5 — Task Bar options

4.4.1 Program Shortcuts in the Task Bar

PILOT automatically detects other Bruker XRD programs installed on your system, and puts shortcutsto them in the appropriate places in the Task Bar. For example, if you have PolySNAP installed, PILOTwill detect it and make PolySNAP available under the “High Throughput Screening” area of the TaskBar.

NOTE: Though PILOT searches for the default

locations of the other programs, specific

paths to the programs may be specified in

the bn-config.py file. For example, a non-

standard installation of PolySNAP may be

specified in bn-config.py as:

programpol ysnap =‘ c: \ \ NonStandardPat h\ \ Pol ySNAP. exe’

Texture

Collect Texture Collect and analyze texture information.

View Textureimages

View, step through, and perform measurements onarea detector frames.

DiffractionSpace Viewer

Create a 3D view in diffraction space based on mea-sured frames.

Instrument

InstrumentControl

Control the goniometer and detector positions.

Icon Task Description


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4.4.2 Stack Bar and Tree View

Right-click on the Task Bar to choose one of two views: Stack Bar or Tree View.

Figure 4.2 — Stack Bar view

In Stack Bar view, click one of the Task Bar sections labeled Single Sample, High ThroughputScreening, Texture, or Instrument to display only the icons belonging to that section. All other Task Baricons will be hidden.

Figure 4.3 — Tree View

In Tree view, sections may be expanded to display their Task Bar icons by clicking the plus or minussign next to the section name.


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4.5 Tool Icon Bar

The Tool Icon Bar provides options for advanced frame viewing and manipulation, and also providesshortcuts to some of the commands available through the Menu Bar. The buttons displayed in the ToolIcon Bar may vary depending on the active module (e.g., frame viewing buttons will not be available forthe Instrument Control module).

Figure 4.4 — Tool Icon Bar

Tool Name Description

“What’s this?” HelpFor context-sensitive help, click on this icon. The mouse cursor willchange to a question mark. Click on any area in PILOT to display ahelp window.

New Open the New Sample, New Tray, or New Tray Template dialogs.

Open Open a list of previously viewed frames.

Save Save the current sample.

Sample Notes Show the Sample Notes window.

Stop Instrument Stop any instrument movement and activity.

Open image Open a collected frame (Alt+O).

The following icons are available for modules that display frames (i.e., XRD2 Eval, View Texture Images, and the Monitor tabfor Collect Sample, Collect HTS, and Collect Texture):

First image Go to the first frame (Alt+shift+left).

Previous image Display the previous frame (Alt+left).

Auto-previousIn movie view, display previous frames in order until the first frame(Ctrl+Alt+P).

Stop In movie view, stop displaying frames (Ctrl+S).

Auto-nextIn movie view, display next frames in order until get to the last frame(Ctrl+Alt+N).

Next image Display the next frame (Alt+right).

Last image Go to the last frame (Alt+shift+right).

Frame display rateIn movie view, set the frame display rate. Increase the frame displayrate by moving the slider to the right.

Previous run Display the previous run (Alt+down).

Next run Display the next run (Alt+up).

Region of interest Tool Select a rectangular region of the frame (Ctrl+R).

Zoom Navigation When a displayed frame is zoomed in, pan around the frame.


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Table 4.6 — Tool Icon Bar button functions

4.5.1 Image Controls

Right-click on the Tool Icon Bar to enable or disable Image Controls, which displays or hides the ToolIcon Bar.

Figure 4.5 — Image Controls enabled

Figure 4.6 — Image Controls disabled

4.5.2 Floating Toolbars and the Line Up Command

The “What’s This?” Help and the Image Controls tools are detachable from the top of the PILOTinterface. If desired, click and hold the mouse on the vertical “handle” on the left side of the tool (Figure4.7). Drag the toolbar to the desired location.

Figure 4.7 — Floating toolbars

To put the tools back on the top of the PILOT interface, simply click on the “handle” and drag the toolsto the top. If the toolbars are positioned unevenly at the top of the PILOT interface, you can align them

by right-clicking on the Tool Icon Bar and choosing Line Up.

4.5.3 Tool Icon Bar Keyboard Shortcuts

Some users may find it easier to use the keyboard rather than the mouse to activate the variousfunctions of the Tool Icon Bar. Key combinations for the icons are given in Table 4.6.

The following icons are available for the XRD2 Eval module:

Wedge Tool Draw a conic integration region on a single frame.

Slice Tool Draw a slice integration region on a single frame or on multiple frames.

The following icons are available for the Diffraction Space Viewer module:

Select RunsSelect runs from the source directory to create a diffraction spaceimage.

CalculateCalculate the diffraction space image based on the loaded frames andparameters.

Tool Name Description

Handles

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4.6 Task Display Area

The Task Display Area is the main area for tasks, user input, and selected output. This area displaysexperiment setup parameters, detector frames, and instrument control options depending on the activePILOT module.

Input fields with a pink background indicate invalid entries. Disabled (grayed out) fields indicate that a

feature is not available (i.e., not supported or dependent on the instrument configuration).

4.7 Image Information Area

The Image Information Area provides data about the currently-displayed image. It contains three tabs:Image Header, Tool Editor, and Cursor Position. The Image Information Area is discussed in detail inSection 6.3.1.

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5.2 Creat ing Trays for Screening

If you are using PILOT for high-throughput screening (Section 9), you will use trays and tray templates to collect your data.

5.2.1 Indi vidual Trays

Creating a New Tray

To create a new tray template, choose Sample > New > Tray... from the Menu Bar or click the New icon

for the same choices.

The New Tray dialog allows you to create a new tray based on an existing Tray Template. As with newsamples, all information about the tray is stored in the specified directory, and access is controlled bythe specified Group.

Figure 5.2 — New Tray dialog

5.2.2 Tray Templates

Each individual tray used in an experiment is based on a Tray Template which defines the number ofrows and columns in the tray.

Creating a New Tray Template

To create a new tray template, choose Sample > New > Tray Template... from the Menu Bar or click

the New icon for the same choices.

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5.3 Closing and Saving Samples

Close the current sample by choosing Sample > Close from the Menu Bar.

You can save the current sample by choosing Sample > Save from the Menu Bar, or by clicking the

Save button in the Tool Icon Bar.

When closing a sample or exiting PILOT, you are prompted to save or discard your changes to thesample before continuing.

Figure 5.5 — Closing Sample dialog

PILOT will not periodically auto-save your information to the Sample Database, so it is recommended tosave your sample periodically.

5.4 Deleting Samples

NOTE: Deleting a sample only removes thesample’s entry in the Sample Database;it does not delete the files (e.g., framefiles, .raw files, etc.) that you havecreated while working with the sample.

To delete a sample from the Sample Database, choose Sample > Arch ive > Delete Samples... from

the Menu Bar. The Delete Sample(s) confirmation dialog opens.

Figure 5.6 — Delete Sample(s) confirmation dialog

NOTE: If you are unable to delete a sample andyou have the access permissions to doso, check that the sample is not stilllocked by PILOT, i.e., that the sample isnot still listed in the Title Bar. Close thesample and try again to delete it.


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5.5 Archiving Samples

Archiving a sample places all of the information associated with the sample—both its Sample Databaseentry and its generated files—into a single location (either a CD-ROM or a .zip archive) so that it maybe retrieved later. Some useful functions of sample archives include:

• Avoiding space concerns on the local machine’s hard drive;

• Creating a library of sample data according to your institution’s archiving procedures;

• Packaging a known group of files for students to restore and work with as part of atraining curriculum;

• Moving data between computers when it may be too slow (or not secure enough) to doso over a network; and

• Data backup and disaster recovery.

To make an archive of the current sample, choose Sample > Archive... > Sample from the Menu Bar.The Archive Sample window opens (Figure 5.7), offering two options for archiving: .zip files or CD-ROMdata.

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5.5.1 Archiving to .ZIP Fi les

1. In the “Archive Sample” window, choose the “To Zip File” tab (Figure 5.7).

Figure 5.7 — Archive Sample window (“To Zip File” selected)

2. In the “Archive File Name” field, choose the desired name and location for the .zip file,

either by typing the name directly into the field or by using the Browse button .

3. Click Estimate. PILOT examines the contents and paths of the files to be archived, andestimates the size of the resulting archive. The results appear in the “Status” window.

4. Click Begin Archiving. PILOT archives the files and then checks the integrity of thearchive, displaying a progress bar and notes in the “Status” window (see Figure 5.7).

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5.5.2 Archiving to CD-ROM

1. In the “Archive Sample” window, choose the “To CD” tab (Figure 5.8).

Figure 5.8 — Archive Sample window (“To CD” selected)

2. Choose the desired CD burner, drive letter, and write speed.

3. Click Estimate. PILOT examines the contents and paths of the files to be archived, andestimates the size of the resulting archive. The results appear in the “Status” window.The Estimate function also gives the number of CD-ROMs required for the archive.

4. Click Begin Archiving. PILOT prompts you to insert a blank CD-ROM.

5. Insert the CD-ROM to start archiving your sample. Progress bars and status data areshown for the total progress, current CD, and current CD buffer. PILOT will prompt you toinsert new blank CD-ROMs as required to complete the archive.

6. When archiving is complete, PILOT shows a window prompting you to take your CD. Doso and click OK.

Figure 5.9 — “Please take your CD” window

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NOTE: If you restore an archived sample usingthe same name as an already-existingsample, the restored sample willoverwrite the already-existing sample inthe Sample Database.

4. Choose the appropriate group for the restored archive in the “Put in Group:” drop-downmenu.

5. Click Restore Archive. A progress bar and status data are shown as PILOT restores thearchive. When the archive is restored, it can be opened from the Sample > Open >Sample... dialog.

6. Click Close to close the Restore Archived Sample window.

5.6.2 Restoring Samples from CD-ROM Archives

1. In the “Restore Archived Sample” window, choose the “From CD” tab (Figure 5.11).

Figure 5.11 —Restore Archived Sample window (“From CD” selected)

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1. The “Using CD Burner:” field should show the drive you wish to restore from. Otherwise,

use the Browse button to locate the drive.

2. Click Get Arch ive Information from CD and insert the archive CD.

3. The archive name appears so that you can check it for name conflicts with the existingsamples in the Sample Database (shown on the right-hand side of the window). If there

is a conflict, you can choose to change the name of the sample in the “Restore As:” field.

NOTE: If you restore an archived sample usingthe same name as an already-existingsample, the restored sample willoverwrite the already-existing sample inthe Sample Database.

4. Choose the appropriate group for the restored archive in the “Put in Group:” drop-downmenu.

5. Click Restore Archive. A progress bar and status data are shown as PILOT restores the

archive. When the archive is restored, it can be opened from the Sample > Open >Sample... dialog.

6. Click Close to close the Restore Archived Sample window.


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5.7 Working with Experiments

Experiments are managed in the Experiments Viewer, located on the right-hand side of the CollectSample and Collect HTS modules. PILOT allows you to create, delete, run, and abort experiments.

5.7.1 Exper iments Viewer

Displays a list of available experiments.

Figure 5.12 —Experiments Viewer


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Table 5.2 — Experiments Viewer items

Item Description

Experiment Name The experiment name.

ActiveCheck or uncheck this checkbox to activate or deactivate theexperiment.

StatusDescribes the current status of the experiment: Idle, Collect-ing, Completed, Error, or Canceled.

Well Color Click here to open a color picker which will allow you toassign a color to the wells in your tray (for CombinatorialScreening only).

At the bottom of the Experiments Viewer are four buttons for managing experiments.

New Experiment Create a new experiment.

Delete Experiment Delete the experiment from a l ist of available experiments.

Run Experiment(s) Start data collection for the experiments marked ‘Active’.

Abort Stop data collection.


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6 Working with Frames

PILOT allows you to automatically integrate an area detector’s 2D data and merge different ranges intoa full diffraction pattern (i.e., a .raw file) as a part of the experiment setup. However, you can still mergeor integrate manually as described in this Section.

With PILOT’s XRD2 Eval or View Texture Images modules, you can perform a variety of functionsincluding integrating single or multiple frames, creating .raw files, exporting .png image files, andviewing intensities on the frame as a 3D histogram:

• The XRD2 Eval module is available in the Task Bar under the Single Sample and HighThroughput Screening categories.

• The View Texture Images module is available in the Task Bar under the Texturecategory.

To begin using the desired module, click on the XRD2 Eval or View Texture Images icon.

Figure 6.1 — XRD2 Eval or View Texture Images icon


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6.1 Opening and Integrat ing Frames

To obtain integrated data from a frame or frames, simply open the frames (Section 6.1.1 or 6.1.2),select the desired region of integration (Section 6.1.3), and finally integrate and export the integratedintensities to a .raw file (Section 6.1.4).

6.1.1 Opening a Frame

1. From the Tool Icon Bar, click the File Open icon .

2. The Choose Image File dialog appears. Choose the desired frame filename and clickOpen . The frame appears in the Task Display Area.

Figure 6.2 — Choose Image File Dialog


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6.1.3 Selecting Parts o f the Image

Once an image is displayed, parts of it can be selected for further processing in three ways: Wedge,Slice, and Region of Interest.

• The Wedge tool is used to select an area of a single image (i.e., one with no framemerging).

• The Slice Tool is used to select an area of a composite image (i.e., one made frommultiple frames). The Slice Tool also works with single images.

• The Region of Interest Tool is used to select a rectangular area of an image. TheRegion of Interest Tool is not used for integrating, but rather for other image operationssuch as Zoom, 3D view, and Pixel Dump (Section 6.3).

Selecting a Wedge

1. From the Tool Icon Bar, select the Wedge Tool .

2. Click and drag the mouse across the image to select the desired wedge. Release themouse when done.

Figure 6.5 — Wedge tool

Selecting a Slice

1. From the Tool Icon Bar, select the Slice Tool .

2. Click and drag the mouse across the image to select the desired slice. Release themouse when done.

Figure 6.6 — Slice tool (composite image shown)


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Masking the Image

Click this option to mask a region of the frame area. Masking the image shrinks the image by equalamounts from top to bottom, but does not change the width of the image.

NOTE: If you export a masked image as a PNG

file, the masked pixels are exported asgray (i.e., no pixels are cropped).

Figure 6.9 — Mask dialog


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6.1.4 Integrating and Saving RAW Files

Right-clicking in the Task Display Area shows the menu in Figure 6.10 (available only when a wedge orslice is selected).

Figure 6.10 —Displayed frame right-click menu

Integrating the Selected Region

Click this option to integrate the region selected by the Slice Tool or Wedge Tool. PILOT displays theresults of the integration as an intensity vs. 2-Theta graph in the Image Information Area’s Tool Editorwindow. The Tool Editor window also shows precise values for 2-Theta, Gamma, and the step size(Figure 6.11).

It is also possible to manually set the range of integration by typing values for 2-Theta min, 2-Thetamax, Gamma start, Gamma end, and Step size into the appropriate fields in the Tool Editor (bottom ofFigure 6.11).

Figure 6.11 —Integrating the selected region

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Create RAW file

Click this option to save integration results as a .raw file, viewable in DIFFRACplus EVA.

Figure 6.12 —Save raw file dialog (non-21CFR Part 11 installations)

NOTE: In 21 CFR Part 11 installations, the .rawfile is saved as an electronic record inthe Electronic Records directoryspecified by the ERService.


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6.2 Frame Viewing Options

6.2.1 Image Brightness and Contrast Controls

While an image is displayed, you can click and drag the sliders at the bottom of the Task Display Areato adjust the brightness of the brightest and darkest pixels.

Moving both of the sliders to the left or right changes the overall brightness of the image, whilechanging the distance between the sliders affects the contrast.

Figure 6.13 —Normal Image (composite image shown)

Figure 6.14 —Brightened Image

White pixel = 9 counts

(too dark to see some rings)

Black pixel= 0 counts

White pixel dragged down to 1 count

Black pixel= 0 counts


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6.2.2 Color Options

Right-click on the color scale at the far right of the Task Display Area to choose different color/viewoptions for displaying the image, or to create a custom color scheme. The default color scheme is “BB”,which simulates the colors of black-body radiation.

NOTE: When there are both bright and darkfeatures of interest in the same image,activate the “Logarithmic” option at thetop of the Color Options menu for bettervisibility.

Figure 6.15 —Color Options menu


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6.2.3 Zooming In on the Image

The Region of Interest Tool allows you to zoom the image based on the region you selected. To zoom inon a part of the image, use the Region of Interest Tool to select an area of the image. Right-click in theselected region to display zoom options for the region:

• Click Zoom + to zoom in so that the selected region fills the Task Display Area.

• Click Zoom - to restore the zoom to the original view.

Zoom Navigation Mode

While zoom is activated, a navigation icon appears in the lower right-hand corner of the TaskDisplay Area.

Clicking and holding the mouse on this button causes a small image navigation window to appear(Figure 6.16) which allows you to rapidly move your zoomed-in field of view around the larger image.

Releasing the mouse button exits zoom navigation mode, but the image remains zoomed in.

Figure 6.16 —Zoom navigation mode

Zoom Navigation Window

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6.2.4 The Fl ip Image Function

Depending on your experimental setup, it may be desirable to flip the image from left to right so that 2-Theta increases in the same direction as your view of the instrument. Right-click anywhere in the image(no selection is necessary) and choose Flip Image to flip the image from left to right.

Figure 6.17 —Flip image

Figure 6.18 —Flipped image


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6.3 Displaying Frame Informat ion

6.3.1 The Image In format ion Area

The Image Information Area provides data about the currently-displayed image. Three tabs in theImage Information Area provide data about the displayed frame (these are the same windows that

appear under the Monitor window when an experiment is in progress):• Image Header: Bruker AXS area detector frame files have a “header” portion that

contains additional information about the image. For more information about the headerand its contents, see Appendix C.

• Tool Edito r: Selecting the Wedge, Slice, or Region of Interest Tool automaticallychanges the active tab to the Tool Editor. The Tool Editor displays integration graphs,information about the selection region, and intensity/angle information at the location ofthe mouse cursor.

• Cursor Position: While information in the Tool Editor is about the selection region,information under the Cursor Position tab is only for the mouse cursor. It gives theposition of the mouse cursor in terms of pixels, angles, and distance across the detector

face, in addition to intensity.The Image Header Tab

The image header tab gives a collapsible overview of all information in the current image’s header (i.e.,measurement conditions). For more information on the Bruker frame header format and content, seeAppendix C.

Figure 6.19 —Image Header (expanded view)

Image Header Right-click Menu

If you right-click in the Image Header window, the following menu will appear:

Figure 6.20 —Image Header right-click window

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Table 6.1 — Image Header right-click menu items

The Tool Edito r Tab

The Tool Editor window displays integration results.

A line appears on the integration graph that represents the location of the mouse cursor within thedisplayed image. By moving the mouse cursor across the displayed image, the line may by positionedto display intensity and angle information.

Figure 6.21 —Tool Editor window

The Cursor Posit ion Tab

The Cursor Position window provides information about the mouse cursor’s current position on theimage (in pixels and 2-Theta) and the count rate per pixel.

Figure 6.22 —Cursor Position window

6.3.2 Disp lay ing Frame Names

Right-click in a displayed image (nothing needs to be selected) and choose Display Frame Names todisplay the current frame name(s). For composite frames, this function displays the names of all of theconstituent frames.

Figure 6.23 —Display frame names

Menu Item Description

Open All Opens all of the nested menus in the Image Header window.

Close All Closes all of the nested menus.

Copy All Copies the contents of the image header to the Clipboard insummary format.

X Y


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6.3.4 Pixel Dump

After selecting part of the image with the Region of Interest tool , right-click and choose Pixel Dump for a pixel map of the intensity of the selected region.

Figure 6.25 —Pixel Dump


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6.4 Example: Integrat ing Single Frames

1. Open a frame (see Section 6.1.1). If you are planning to process a single frame (i.e., no

frame merging), select the Wedge Tool .

2. Click and drag the cursor from left to right. A conic integration region will appear(Figure 6.26).

Figure 6.26 —Setting up an integration range

3. Adjust the integration parameters manually in the Tool Editor tab or right-click and select Ad just reg ion. Adjust the sliders to set the integration range for 2-Theta and gamma.Close the box when done.

Figure 6.27 —Adjust the integration range

4. Right-click and choose Integrate to integrate in the region selected. The integrationgraph appears in the Tool Editor tab.

5. Right-click and choose Create Raw File to save the integrated data as a .raw file forevaluation in EVA.

6. Enter the file name and click Save.

7. If you have DIFFRACplus EVA installed, click the EVA icon to import the .raw file into EVA.

8. To proceed, refer to M85-Exx002 DIFFRACplus EVA User Manual.

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6.5 Example: Merging and Integrating Multiple Frames

1. Open several frames as a composite frame (see Section 6.1.2).

Figure 6.28 —Load multiple files/frames

2. After frame processing stops, select the Slice Tool and click and drag the cursor fromleft to right to select an integration region.

Figure 6.29 —Integrate multiple frames

3. Right-click and select Ad just reg ion. Adjust 2-Theta min, 2-Theta max, and the slice’s

height in pixels. Close the box when done.4. Right-click and select Integrate to integrate the data in the selected region.

5. Right-click and select Create Raw File to save the integrated data as a .raw file forevaluation in EVA.

6. Enter the file name and click Save.

7. If you have DIFFRACplus EVA installed, click the EVA icon to import the .raw file into EVA.

8. To proceed, refer to M85-Exx002 DIFFRACplus EVA User Manual.


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7 The Instrument Control Module

Regardless of what kind of experiment you are doing, it is important to be able to communicate directlywith your instrument from within PILOT. The Instrument Control module, available under PILOT’s“Instrument” category, allows you to:

• Control your instrument directly (including “homing” the axes);

• Place the instrument into Manual mode; and

• Check and adjust important parameters such as axis speeds and limits.

7.1 Instrument Control

Select Instrument from the Task Bar. Within Instrument, click the Instrument Control icon.

Figure 7.1 — Instrument Control icon

Four tabs appear in the Task Display Area:

• Manual• Update/Home

• Axes Limits

• Axes Speeds


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7.1.1 Manual

The “Manual” tab allows you to move drives to align the sample, open or close the shutter, viewhardware setup parameters, and place the system in manual mode.

Figure 7.2 — Manual


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Table 7.1 — Manual

Manual

Goniometer Axis control

Drive

Drives or sets an axis to the requested position.

NOTE: A non-motorized axis’ name isshown in angled brackets. Auxiliaryaxes that are not available areshown in gray (see Figure 7.2).

Drive All Drives all drives from their current positions to the requested positions.

Clear All Requested Positions Resets all requested values.

Park Moves all axes to predefined safety positions.

ManualToggles between manual control mode and software control mode. This feature is availableonly for instruments that are equipped with a manual control box.

OpticalIf you have a GGCS controller without a laser/video alignment system, toggles betweenoptical control mode and software control mode.

Open/Closed Opens and closes the respective X-ray shutter.

Video Laser Turns the alignment laser on and off, if present.

Set Generator Changes and sets the generator settings.

Set Frame SizeChanges the frame size in pixels. Generally, powder applications use 1024 pixels and singlecrystal applications use 512 pixels.

AbortStops the measurement and movement of all drives. Closes shutters and turns off the align-ment laser.

Shutters

Safety Shutter button Toggles the safety shutter ( i.e., the main shutter).

TIming Shutter button Toggles the timing shutter (i.e., the “fast” or “smart” shutter).

Attenuator Shutter button Toggles the attenuator.

Digital I/O lines

Video Laser buttonSwitches the laser on and off. This button is enables only for instruments that are equippedwith an alignment laser.

Other buttons for auxiliary functions may be available under the “Digital I/O Lines” area.

Generator

Generator values Sets the “requested” generator voltage and current in kV and mA.

Set generator

Sets the generator to the requested power.

NOTE: The user may not be allowed to changethis setting depending on his or herlogin account type.

Frame Size

Frame Size values Sets the “requested” detector frame size in pixels.

Set Frame Size

Sets the detector to the requested frame size.

NOTE: The user may not be allowed tochange this setting depending on his orher login account type.

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7.1.3 Axes Limits

The “Axes Limits” tab allows you to set and change software limits. Often, the current software limits areset conservatively to prevent all possible collisions. Some specimens or data requirements, however,may force you to collect data with components of the instrument nearly touching. For these cases, youmay need to relax the current software limits. Conversely, large samples may reduce your axes’operating ranges and you may wish to restrict your software limits to be safe.

You are not allowed to set the limits beyond the absolute limits defined by your instrument manager(using BCP), nor can you change the limits so that the goniometer is in collision. Before changing thelimits, it is important to understand hardware limits, software limits, coupled limits, and how BIS usesthese limits.

Hardware Limi ts

Hardware limits are physical switches along the travel of an axis (or coupled axes). The goal is toprevent the axis motor from running into a physical barrier—which can cause an alignment issue—andfrom continuing to provide current to a stuck motor (which can damage the motor). Whenever thegoniometer controller hits a hardware limit switch, that axis (or axes for a coupled hardware limit switch)is immediately stopped. Because of the fast stop, all affected axes become unreferenced, forcing you to

update and home the axes. For linear axes, hardware limit switches are generally placed at the ends ofthe physical travel for that axis. For rotary axes, hardware limits are placed to prevent collision withmounted instrument components, such as the microscope or collimator mount. These physical limitswitches are factory-placed and should not be changed.

Software Limits

Software limits should prevent the instrument from hitting a hardware limit switch and any stationaryobject. Because the detector distance affects the travel range of the detector arm (either Theta2 or 2-Theta), that axis’ software limits are a function of the detector distance. Some rotary axes, such as Phi,can spin indefinitely. The special limit values of 0.0 to 0.0 mean unlimited motion on a rotary axis.

Coupled Software Limits

Coupled software limits should prevent movable components from colliding. For Theta-Theta, thecoupled limit is θ1 + θ2, which prevents the tube housing and detector from colliding. For Bragg-Brentano, the coupled limit is ω - 2θ, which prevents the goniometer stage and detector from colliding.Both coupled limits are dependent on the detector distance. For coupled limits, the values of the twoaxes are combined, and then that value is compared against their coupled limits according to:

Low limit ≤ θ1 + θ2 ≤ high limit

Low limit ≤ ω - 2θ ≤ high limit

BIS checks the software axes’ limits before any drive request. The starting position, ending position,and drive path must pass the software limits check before BIS starts the drive operation. When using

the manual control box, the firmware will check the software limits as the axis is moving and will stopthe axis when the software limit is reached (or sometimes, slightly passed). You should always back offany axis beyond the software limits before leaving manual mode as BIS will refuse to start any drive ifan axis is already in collision.


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BIS will automatically update some axes’ limits whenever the detector distance changes. For Theta-Theta systems, the updated limits are Theta2 and Theta1+Theta2. For Bragg-Brentano systems, theupdated limits are 2-Theta and Omega-2-Theta. Therefore, your changed limits for these axes are onlyvalid until the detector distance moves.

Figure 7.4 — Axes Limits tab

Table 7.3 — Axes Limits

CAUTION!

To avoid instrument collision, keep theinstrument’s movement path in mind whenchanging values in this window!

Axes Limits

Set All Limits Set the instrument limi ts to the “Current Low Limit” and “Current High Limit” sett ings.

Copy Maximum To CurrentLimits

Copies the maximum limits to the current limits. Subsequently pressing the Set All Limits button resets all current limits to their maximum values.


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7.1.4 Axes Speeds

The “Axes Speeds” tab displays information about the axes’ maximum drive speeds. Axis speeds arenot editable in PILOT (they are set in BCP).

Figure 7.5 — Axes Speeds tab


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8 Single Sample

XRD2 characterizations of single samples (as opposed to groups of samples in a combinatorialscreening arrangement) are handled completely within PILOT’s Single Sample category of softwaremodules. The Single Sample category, accessible from PILOT’s Task Bar, contains two modules:

Collect Sample and XRD2 Eval.

8.1 Collect Sample

Figure 8.1 — Collect Sample icon

1. Once you have created a sample, click the Collect Sample icon under the Task Bar’sSingle Sample category. The Collect Sample module opens.

NOTE: If you are not connected to BIS, theInstrument Connection dialog will

prompt you to connect beforeproceeding.

2. You are prompted to enter an experiment name for the sample. Enter a name and clickOK.

Figure 8.2 — New Experiment dialog

The Collect Sample module opens. The Collect Sample module main window contains three tabs, onefor the each phase of the experiment:

• Sample Setup — used to describe the sample, its mounting method, and its datacollection mode (i.e., transmission, reflection, or both).

• Experiment Editor — used to describe the conditions of the experiment such as filenames, goniometer positions, and scan parameters.

• Monitor — gives a real-time view of the area detector frames as they are collectedduring the experiment. You can also examine the frames with the Region of Interest Tool.


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8.1.1 Samp le Setup Tab

Enter information for the sample and describe it in the Sample Description window. Choose anexperiment type based on your experiment setup and proceed to the Experiment Editor tab.

Figure 8.3 — Sample Setup tab

Table 8.1 — Sample Setup tab


Sample Information

Sample NameThe sample name as entered in the Sample > New > Sample... dialog. The sample name cannotbe changed after the sample is created.

Sample Number You may assign a number to the current sample by entering the desired number in this field.

Sample Description

Sample DescriptionA Sample Description window is provided for miscellaneous text information. For single samples(not for trays), the first 72 characters of the first 8 lines are placed into the frame file header andalso into the .raw file.

Sample Mounting

Sample Mountingpreset buttons

Choosing one of the preset buttons applies appropriate presets to the Mode area. These presetvalues also help to specify default settings for data collection.

The Other button allows you to input values directly into the Sample Shape, Mode, and Direction

areas.Displayed buttons may vary depending on your goniometer configuration.

Mode

Transmission X-rays are transmitted through the sample to the detector.

ReflectionX-rays are reflected from the sample to the detector, which may be on the same side of the sam-ple as the source.

Both The data collection mode has characteristics of both transmission and reflection mode.


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8.1.2 Exper iment Ed itor Tab

Filename Generator

The top of the Experiment Editor tab contains the Filename Generator, in which you define a framename according to a Base File Name, Run or Target number, and frame number. The “First Filename”field shows an example of the frame naming convention, along with the location to which the frames will

be saved.

The Experiment Name is displayed directly beneath the Filename Generator.

Figure 8.4 — Experiment Editor: Filename Generator, Experiment Name, and Goniometer Positions

Frame file naming conventions in the Filename Generator • Single Sample Module — Frame file names follow this convention:

base_r r _ f f f f . gf rm, where base is the base file name, r r is the run number ortarget number (01 to 00), and f f f f is the frame number (0001 to 9999). The user entersthe name of the first frame file, and the frame number is automatically incremented byone if a data collection results in multiple frames being collected.

• High Throughput Screening Module — Frame file names follow this convention:base_wel l _r r _f f f f . gf rm, where wel l is the well name (the rest is the same as forthe Single Sample Module). The well name is configured in the tray template.

Goniometer Positions

Read the projected positions of the goniometer during the experiment by clicking the GoniometerPositions button. This is especially useful if you wish to set up your experiment parameters to collectthe widest angle range without causing a goniometer collision.

Figure 8.5 — Detector and Goniometer Positions window

If the goniometer positions calculated by PILOT are illegal (i.e., outside the goniometer’s limits), theywill be displayed in gray fields. If desired, you can edit the goniometer positions directly by clicking inthe appropriate field.

You can also use the buttons along the bottom of the Detector and Goniometer Positions window to addand remove additional positions for the experiment.


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Table 8.3 — Experiment Editor: Detector Angles/Sample Positions tab


2-Theta

2-Theta Startand End

Starting and ending 2-Theta of interest. Used to calculate frame angles and integration range for .raw f ile.

Pixel Overlap Amount of overlap between two successive frames.

Create RawFile

If activated, the experiment will automatically integrate all frame files generated by the experiment usingthe 2-Theta range (start and end) and integration step size. The gamma range is -360° to +360°.

Integration StepSize

If “Create Raw File” is activated, the size of the integration steps. Integration step size is a function ofdetector frame size and distance.

Omega

MaximumIncident Angle

If activated, the collection strategy collects data at the maximum angle that will not cast a shadow on thedetector. Gives the sharpest and most accurate peak profiles.

Disabled if the calculated detector and goniometer positions have been overridden. Click the Reset buttonon the detector and goniometer positions dialog to restore the calculated positions.

Bisecting Mode

Omega is set to half of 2-Theta. Gives the most accurate peak intensities for routine quantitative analysis.


Fixed Omega

Omega remains at a fixed angle through the 2-Theta range.


Sample Rough-ness

If the sample surface is rough, the incident angle Omega or Theta1 will be adjusted upward by the amountof roughness (in degrees) to compensate for the angle of the shadow caused by the sample roughness.

Resolution

Frame Size Select the frame size for your collected frames.

Distance Specify the distance from the detector to the sample.

Type D8 SCREENLAB systems have an option to collect either XRD data or Raman spectroscopy data.

Goniometer Positions

Current andStart Positions

These columns display the current position of the sample, and lets you specify initial position values forthe scan.

Use CurrentPositions

Loads the current position of the sample into PILOT.

Auto-ZAlignment

Uses the VIDEO program and BIS to drive the Z-axis until the alignment laser spot is centered in VIDEO’scrosshair reticle. The Z-ax

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