Database Viewer
version 2.0.4 rev 27 November 2014

Software Guide
andor.com© Andor Technology 2014

Database Viewer
Table of Contents
Table of Contents .......................................................................................................................................................... 2
SECTION 1:

THE DATABASE VIEWER ............................................................................................................................. 4

1.1

Introduction ...................................................................................................................................................... 4

1.2

Organization of Datasets – Security, Tables and Tabs ....................................................................................... 5

1.3

Terminology ...................................................................................................................................................... 5

SECTION 2:
2.1

VIEWING DATASETS ................................................................................................................................... 6

Opening Datasets .............................................................................................................................................. 6

2.1.1 Database Window: Data Tab ............................................................................................................................. 7
2.1.2 Database Window: Data Audit Tab .................................................................................................................... 8
2.1.3

Database Window:Session Record Tab ...................................................................................................... 9

2.1.4 Database Window: System Audit Tab ................................................................................................................ 10
2.1.5 Database Window: Decode Tab ......................................................................................................................... 11
2.1.6 Database Window: Summary Tab...................................................................................................................... 11
2.1.7 Database Window: META Tab ........................................................................................................................... 12
2.2 DBV Menu: File...................................................................................................................................................... 13
2.2.1 File: Open Database ........................................................................................................................................... 13
2.2.2 File: Close Database ........................................................................................................................................... 13
2.2.3 File: Make Standalone CD .................................................................................................................................. 13
2.2.4 File: Export ......................................................................................................................................................... 14
2.2.5 File: Print Table .................................................................................................................................................. 15
2.2.6 File: Merge Databases ........................................................................................................................................ 15
2.2.7 File: Exit .............................................................................................................................................................. 16
2.2.8 File: Recent File List ............................................................................................................................................ 17
2.3 DBV Tab: Graphs ................................................................................................................................................... 18
2.3.1 Graphs: Histogram ............................................................................................................................................. 18
2.3.2 Graphs: 3D Histogram ........................................................................................................................................ 20
2.3.3 Graphs: Bar Chart ............................................................................................................................................... 22
2.3.4 Graphs: Response Curve .................................................................................................................................... 23
2.3.5 Chart Menu ........................................................................................................................................................ 26
2.4 DBV Tab: Gallery ................................................................................................................................................... 27
2.4.1 Gallery ................................................................................................................................................................ 27
2.4.2 Gallery Options .................................................................................................................................................. 29
2.5 DBV Tab: Data ....................................................................................................................................................... 32

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2.5.1 Data: Create Summary Table ............................................................................................................................. 32
2.5.2 Data: Decode Database(s).................................................................................................................................. 35
2.5.3 Data: View Outliers ............................................................................................................................................ 40
2.5.4 File Menu for View Outliers ............................................................................................................................... 41
2.5.5 Exclude Data....................................................................................................................................................... 42
2.5.4 Show Database................................................................................................................................................... 43
2.6 DBV Tab: Windows ................................................................................................................................................ 44
2.6.1 Windows: Tile..................................................................................................................................................... 44
2.6.2 Windows: Cascade ............................................................................................................................................. 44
2.7 DBV Menu: Help .................................................................................................................................................... 44
2.7.1 Help: Help........................................................................................................................................................... 45
2.7.2 Help: About ........................................................................................................................................................ 45
SECTION 3:

INSTALLING THE SOFTWARE .................................................................................................................... 46

SECTION 4:4 DEFINITIONS AND INFORMATION ON DECODING DATASETS AND CREATING SUMMARY TABLES ..... 47

References .................................................................................................................................................................. 48

Contact Information:www.andor.com/contact_us/support_request

This version updated for Database Viewer 2.0.4, revised 27 Nov 2014

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SECTION 1: THE DATABASE VIEWER
1.1 Introduction®

The Database Viewer (DBV) is supplied with certain products, including Komet ® and Komet GLP. This
software saves data in two formats:•Tab-delimited format, which can be read by standard spreadsheet programs such as Microsoft
Excel. Excel macros are provided to ease the analysis and presentation of this data.

•

A Database format, which includes images and data. The Database Viewer is the means to view,
analyse and present data from these files. For GLP operation Study and Scoring audit trails canalso be viewed.

The DBV is supplied via download from my.andor.com or on a separate installation CD and is installed as
described in Appendix 1. The DBV is opened from the Kinetic Program Group and provides the following
functions:•

Load and View Datasets containing images and data from a group of specimens.

•

Datasets usually contain all the data from an exposure group.

•

View audit trails on data, scoring sessions, study information and QC.

•

Present data for comparison in graphical forms including Histograms and Response
Charts.

•

Decode Slide or specimen IDs into Dose or Exposure groups to support blind scoring.

•

Present Data Summaries compatible with international guidelines for statistical analysis.

•

Create Image Galleries to present the comets from complete or a subset of theDataset.

•Create a stand-alone CD, which includes the selected Dataset(s), DBV program and all necessary
support files to run DBV on any Windows 7 PC.

Thus, DBV provides a powerful and easy means to review, present and prepare your data for statisticalanalysis. Further, it provides a means to distribute Study data in the form of stand- alone CDs containing
Datasets and all the necessary tools for review and presentation to colleagues, Quality Assurance
Personnel, sponsors and reviewers.
Database Viewer can be distributed freely, without restriction by authorized license holders of our software.
We hope you find the product both easy and powerful to use and thank you for choosing our products.

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1.2 Organization of Datasets – Security, Tables and Tabs
Datasets are databases named with either an mdb or kdb extension. Mdb files are readable in Microsoft
Access. You should be aware that opening a file in Access before scoring is completed will damage its
electronic signature and render the file unusable for GLP work. We recommend you use ONLY the DBV for
working with these files.
The Dataset contents are organized into several tables, and each table is presented on a different tab in
DBV, as described in detail in section 2.1. GLP and non-GLP Datasets are both produced by Komet products
depending on the mode of operation specified. The GLP Datasets will contain additional tabs for Audit
Trails - information gathered during the scoring process, when the Datasets are recorded.
Datasets can be decoded and analysed to generate additional data such as Statistical Summary data. Whenyou operate in this way DBV will create a copy of the original Dataset, to maintain the integrity of the RAW
data. In the copied Dataset it will add new tables, visible as extra tabs in DBV. These will contain additional
information about the Decode and/or Data Summary actions and results.

1.3 Terminology
In the following descriptions of the DBV Software, we use some terms to explain functions in the software
which may have specific meaning. We use these terms to exemplify, not tolimit the application of the product. These terms include:•

Dose and Dose Groups which can equally refer to Exposure and Exposure Groups.

•

Database and Dataset are used to refer to a collection of data organized in tables readable by the
DBV.

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SECTION 2: VIEWING DATASETS
DBV enables datasets (GLP and Research formats) to be viewed for analysis and auditing purposes.

2.1 Opening Datasets
Click the Open Database button on the File tab:

Or from the File Menu select File then select Open Database (Section 2.2.1), this will display a file open
dialogue box where the user can navigate to the appropriate folder and select a Dataset to open.

Figure 2.1.1 Opening a Database
The user will then be prompted to enter the password for the Dataset.

Figure 2.1.2 Enter Password

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The Dataset is then presented as shown in Figure 2.1.3. The Database Window has four tabs in the GLP
version. These are Data, Data Audit, Session Record and System Audit. In the
Non-GLP version, all of these tabs will not be present. Additional tabs for Decode and Summary are added
to the Decoded Dataset once they are created through the appropriate functions (Section 2.5.2).

2.1.1 Database Window: Data Tab

Figure 2.1.3 The Database Window Data Tab
The upper pane of the Data Tab displays the data obtained from your experiment. Each row of data
displays the ID of the image from which data was obtained, the Slide ID and all the values for each analysis
parameter.
When you click on a row of data, the image from which the data was obtained is displayed in the lower
pane along with a calibrated ruler to show comet lengths.

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2.1.2 Database Window: Data Audit Tab

Figure 2.1.4 The Database Window Data Audit Tab
The Data Audit Tab (Figure 2.1.4) provides a record of operator actions during the scoring process. The
Cell ID, Data ID, Action, and reasons are listed for any changes made throughout the study.

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2.1.3 Database Window:Session Record Tab

Figure 2.1.5 The Database Window Session Record
The Session Record Tab (Figure 2.1.5) provides information on all of the scoring sessions. The user namecorresponding to each scoring session, the session action, the reason for suspending the scoring session,
start and end dates, times, Slide IDs and Scoring Protocol are presented.

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2.1.4 Database Window: System Audit Tab

Figure 2.1.6 The Database Window System Audit Tab
The system Audit Tab provides information for all tracked changes made to the Datasets and Protocols(Figure 2.1.6). It also provides information relevant to the QC Audit Trail and the QC Audit Details.

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2.1.5 Database Window: Decode Tab

Figure 2.1.7 The Database Window Decode Tab
The Decode Tab is added to the Dataset window once a decode is performed as shown in Figure 2.1.7.
However, this tab only appears in the new dataset created by the decode operation. The new dataset nameis derived from the original as follows:
Original Name

Decoded Name

Duodenum_RAW.kdb → Duodenum_RAW_DECODED.kdb
This tab provides all information relating to the decoded dataset. For information on how to decode a
database (dataset) see Section 2.5.2.

2.1.6 Database Window: Summary Tab

Figure 2.1.8 The Database Window Summary Tab
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The Summary Tab is added to the Database window after a summary is performed. This Tab is only visible
in the new dataset created through the decode operation as described in the previous section. Additional
summaries can be performed and are subsequently added to the Database window as shown in Figure
2.1.8. For more information on how to create a Summary Table see Section 2.5.1.

2.1.7 Database Window: META Tab
This has no experiment data but contains Komet application information that is useful for technical support.

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2.2 DBV Menu: File
When the DBV application is running, the relevant menus will be active. Their exact content depends onwhich window has focus. When a Dataset Window has focus or no Dataset is open, the menu items shownin Figure 2.2.1 are available. When other types of window such as the Gallery and Chart windows havefocus the menu items on view will change (Sections 2.4.2 and 2.8).

Figure 2.2.1 The File Menu

2.2.1 File: Open Database
Selecting Open Database displays a standard Window’s Load File dialogue, from which you should select the Dataset
to open. You can open multiple Datasets and manage or compare their contents. The Datasets will be presented as
explained in Section 2.1.

2.2.2 File: Close Database
Selecting Close Database closes the currently selected Dataset.

2.2.3 File: Make Standalone CD
Selecting Make Standalone CD from the file menu will open a dialogue box allowing the user to select thelocation to copy the files (Figure 2.2.2). Once a location is selected, the database and DBV files are copied
to the selected location (i.e. CD) that can be opened on any Windows 7 computer.

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Note: If a CRW drive is selected, a formatted CD is required. CRW formatting instructions are
dependent on the software being used.

Figure 2.2.2 Select Drive for Standalone CD

2.2.4 File: Export
The Export feature enables the user to export Database File (*.kdb) to MS Access (*.mdb) file (Figure 2.2.3). Support
for other database platforms may be added in future.

Figure 2.2.3 File Export

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2.2.5 File: Print Table
Selecting Print Table from the file menu allows the user to print tables from the currently selected Dataset. All
Tabs in the selected Dataset will be listed as shown in Figure 2.2.4. Select the Tab you wish to print and astandard print dialogue box will open allowing for printer selection and properties.

Figure 2.2.4 Print Table

2.2.6 File: Merge Databases
Selecting Merge Databases from the file menu enables user to merge several open Datasets into a new Dataset.
Select the open Datasets to merge by clicking on the dataset(s) or by using the Select All or Deselect All
buttons. Selected Datasets will have their checkboxes labelled with a tick. You can change the order of theDatasets by using the Move Up and Move Down buttons.

Figure 2.2.5 Select Datasets to Merge
Press OK to continue.

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Figure 2.2.6 Merge Databases Message
You will then be prompted as seen in Figure 2.2.6. Selecting No will exit the process. Selecting Yes will merge
the databases and open a Save As dialogue box (Figure 2.2.7) allowing you to name the new file.

Figure 2.2.7 Save As

2.2.7 File: Exit
Selecting Exit will close all open Datasets and exit the DBV application.

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2.2.8 File: Recent File List
This feature shows the 5 most recently opened Datasets at the bottom of the menu as shown in Figure
2.2.8. Click on a file to reopen the Dataset.

Figure 2.2.8 Recent File List

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2.3 DBV Tab: Graphs

Figure 2.3.1 Graphs Tab
From the Graphs tab, you can select a method to present the data in a graphical form.
Note - When a Chart Window has focus, different menus are available (see Section 2.3.5).

2.3.1 Graphs: Histogram

Figure 2.3.2 Histogram Dose Group Selection
When a Dataset is open and selected, clicking on Histogram from the Graphs menu displays adialogue box (Figure 2.3.2) which allows selection of the Specimens or Dose groups for which you
wish to see a histogram plot.
The Select All and Deselect All buttons can also be used. When you press OK a histogram window
will open for each selected dose.
The Histogram dialogue box shown in Figure 2.3.3 has many controls to format the histogram
presentation to your needs.
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From the dropdown list shown in Figure 2.3.3, select the parameter for which you want to display ahistogram. All analysis parameters can be selected for review in the histogram.
Range Minimum and Maximum Settings
The Min and Max values are displayed on the left of the dialogue box (Figure 2.3.3) these are theminimum and maximum values calculated from all the cells scored in that specimen or group.

Figure 2.3.3 Histogram
The text boxes are used to enter the minimum and maximum values for the bins to display on the
Histogram. You can restore the computed Min and Max values from the current sample at any time bypressing the Use Min/Max button.
Set Defaults
You can also set up Default Minimum and Maximum values for the histogram bins. To do this, enter
the desired values into the Minimum and Maximum text boxes and press the Set Default button. You
can then select these values at any time by pressing the Use Defaults button. This allows you to fix
settings for standardized reporting of data with different ranges i.e. most real data.
Number of Bins
Enter the Number of bins - the x-axis will be split into a number of divisions equal to the value
specified here. (Note that there will be two additional bins, one containing all valuesbelow the minimum
bin and the other with data above the maximum. These register any data that lies outside of thespecified minimum and maximum values).

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Show as Percentage
When selected, the data will be displayed as a percentage of the number of cells rather than displaying
the actual frequency of data. This presentation is useful for standardizing the presentation of data from
specimens in which a different number of cells or fields was scored.

2.3.2 Graphs: 3D Histogram

Selecting 3D Histogram from the Graphs tab opens a dialogue box which is used to create a 3D
presentation. This allows you to open multiple Datasets, which is useful for data comparison. The first
dialogue box will appear as shown in Figure 2.3.4. Click in the checkboxes to select the datasets toinclude in the histogram or use the Select All and Deselect All buttons.
You can change the order that the datasets will be displayed in the histogram using the Move Up andMove Down buttons.
Press OK to continue.

Figure 2.3.4 Select Dataset(s) for 3D Histogram
A dialogue box will then open for each selected Dataset and list the available doses in that dataset.
You can change the order of the doses as above or use the Select All and Deselect All buttons.
Selected Datasets will have their checkboxes labelled with a tick.

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Select the doses to include in the histogram (Figure 2.3.5) and press OK to continue.

Figure 2.3.5 3D Histogram Dose Group Selection
After selecting the doses from the final dataset, the histogram will be displayed (Figure 2.3.6).

Figure 2.3.6 3D Histogram
From the dropdown list, select the parameter for which you want to display a histogram. The Min andMax values are displayed on the left of the dialogue - these are the minimum and maximum values
calculated from all the comet cells scored in the selected doses.

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Set Defaults
You can also set up Default Minimum and Maximum values for the histogram bins. To do this, enter
the desired values into the Minimum and Maximum text boxes and press the Set Default button. You
can then select these values at any time by pressing the Use Defaults button. This allows you to fix
settings for standardized reporting of data with different ranges i.e. most real data.
Number of Bins
Enter the Number of bins - the x-axis will be split into a number of divisions equal to the value
specified here. (Note that there will be two additional bins, one containing all values below theminimum bin and the other with data above the maximum. These register any data that lies outside of
the specified minimum and maximum values).
Show as Percentage
When selected, the data will be displayed as a percentage of the number of cells rather than displaying
the actual frequency of data. This presentation is useful for standardizing the presentation of data from
specimens in which a different number of cells or fields was scored.
3D View Angles
You can change the 3D view angle by holding down the left mouse button over the 3D Histogram.
Move the mouse to rotate the graph to the desired position.

2.3.3 Graphs: Bar Chart

When a Dataset is open and selected, clicking on Bar Chart from the Graphs tab displays a dialogue
box in which all the doses in the Dataset are listed (Figure 2.3.7). Select the doses for which you want
to display a Bar Chart (selected doses have their checkboxes labelled with a tick). The Select All andDeselect All buttons can also be used.

Figure 2.3.7 Bar Chart Dose Group Selection

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When you press OK a Bar Chart will open for each selected dose as shown in Figure 2.3.8.
From the dropdown list in Figure 2.3.8, select the parameter for which you want to display a bar chart.
Values are displayed for each cell scored in that dose. If Use record name on x axis is selected, each
set of data is labelled with its source image. If it is not selected, they are labelled according to theiridentifier (a number determined by the order in which they are scored during the experiment).

Figure 2.3.8 Bar Chart

2.3.4 Graphs: Response Curve

Figure 2.3.9 Select Dataset(s) for Dose Response Curve

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Response Curves are used to compare data from different doses in the Experiment. If you selectResponse Curve from the Graphs tab, a dialogue box will list all opened Datasets (Figure 2.3.9). Clickin the checkboxes to select the Datasets to include in the histogram or use the Select All or DeselectAll buttons. You can change the order that the Datasets will be displayed in the curve by using theMove Up and Move Down buttons.
Press OK to continue.

Figure 2.3.10 Dose Selection for Response Curve
A dialogue box will then open for each selected Dataset and list the available doses in that Dataset(Figure 2.3.10.). You can change the plotting order as above. Select the doses to include in the
Response Curve or use the Select All or Deselect All buttons. Press OK to continue.

Figure 2.3.11 Select Statistics
Select the statistics you wish to plot, selected statistics have their checkboxes labelled with a tick(Figure 2.3.11). A Response Curve will be plotted for each selected statistic. Options atthe bottom of
the dialogue box allow the inclusion of error bars on the plots. When you have made your selection
press OK to continue.

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Figure 2.3.12 Dose Response Curve
From the dropdown list, select the parameter for which you want to display a Response Curve (Figure
2.3.12).
The statistic for each selected dose is represented by a point on the curve - the points are colour
coordinated and a key below the curve tells you which colour corresponds to which dose.

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2.3.5 Chart Menu
Different menus are available when the Histogram, 3D Histogram, Bar Chart or
Response Curve dialogue boxes are selected (Figure 2.3.13).

Figure 2.3.13 The Chart Menu Bar
Options
Defines the style of the selected chart. This includes the format, colour and position of titles and othertext, and the background colour for the selected chart. The style will be remembered for the current
session of the Database Viewer.
Series Colour
Allows you to select the colour in which to display the data on the selected chart.
Print
Opens the Printer Setup dialogue, from where you can print the selected chart.
Show Database
Places the Database Window on top of all other Windows.

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2.4 DBV Tab: Gallery

Figure 2.4.1 The Gallery Tab

2.4.1 Gallery

Selecting Gallery opens a dialogue box which displays messages depending on whether the dataset
has been decoded or not. If the data set has not been decoded a list of all slide names will appear(Figure 2.4.2) and if the dataset has been decoded the list of dose groups will appear (Figure 2.4.3).
Select the slides or dose groups to view by selecting them individually or by using the Select All andDeselect All buttons. Selected slides or groups are labelled with a tick.

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Figure 2.4.2 Gallery Slide Selection

Figure 2.4.3 Gallery Dose Group Selection
Press OK to continue. If Datasets are large, the gallery may take a few minutes to open.
The Image Gallery shows an image of every cell scored in the selected slides or dose group(s) in theupper pane. Calipers (vertical red lines) show the start and end of the comet Head and Tail regions as
analysed by Komet®. If ‘Head Ellipse’ is selected in Comet Options, then an ellipse will be shown
delineating the Head region. Deleted Cells are also recorded in the Gallery, but to indicate theirrejection from data analysis they are shown with a single diagonal Red Line indicating their status asshown in Figure 2.3.4. If Image Numbers are selected, Red numbers are shown on the individual
images, indicating the data position in the current Dataset.

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Figure 2.4.4 The Gallery Window
The lower pane shows the ID (a number determined by the order in which it was scored during theexperiment), the Session in which the cell was scored, the Slide Number, Slide Replicate, and all thevalues for each analysis parameter. The lower pane will also show if the selected cell is a Deleted
Record and if so the number referring to the Reason it was deleted as shown in Figure 2.4.4.

2.4.2 Gallery Options
When the Gallery dialogue box is open, the available menus will change.

Figure 2.4.5 The Gallery Menu Options
Printing the Gallery
Selecting Print from the options menu opens the Image Print Setup dialogue box. This allows theGallery to be printed on a user-defined number of pages by setting up the comet image density. The
Number of Pages will change as the Number of Columns and Rows per page is adjusted.

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Figure 2.4.6 Image Print Setup
Clicking on Setup… opens the printer setup dialog

Once the printer has been setup, click OK to confirm the settings.
When the Image Print Setup dialog is visible, press Print to accept your selection and being printing.

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If the assigned number of rows and columns per page is too large, an error message will be received
and allow the user to re-define the parameters (Figure 2.4.7).

Figure 2.4.7Selectedparameterstoo large error message
Image Numbers
This can be toggled on and off by a mouse click. When on, the image number is displayed in the top
left of each image (Figure 2.4.4). They are numbered in the order that they were opened or acquired
during the scoring session.
Show Database
The Window containing the Dataset will be displayed on top of all other windows.

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2.5 DBV Tab: Data

Figure 2.5.1 The Data Tab
Note: See Appendix 2 for definitions and more information on Decoding Datasets and Creating
Summary Tables.

2.5.1 Data: Create Summary Table

Note: A Dataset should be decoded before selecting Create Summary Table (See Decode
Databases(s) Section 2.5.2).
When a Decoded Dataset is open and selected, clicking on Summary Table from the Data Menu
displays a dialogue box in which all the doses in the decoded database are listed (Figure 2.5.2). Selectthe doses you want to display in a Summary Table (selected doses have their checkboxes labelledwith a tick). The Select All and Deselect All buttons can be used for selecting groups. You canchange the order that the doses will be displayed in the Summary Table by using the Move Up andMove Down buttons.

Figure 2.5.2 Dose Selection for Summary Table
Press OK to continue.
A Summary Table of DATA dialogue box will open that allows you to select the Required Parameters
to measure based on what is required for data presentation (Figure 2.5.3).
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Select the desired Statistics for both the Individual and Dose/Group and the number of decimal places
for data presentation.

Figure 2.5.3 Summary Table Window
Once all parameters are selected, press the Update button. This will update the bottom window asshown in Figure 2.5.4.

Figure 2.5.4 Updated Summary Table Window

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Once the table is updated any changes can be made and viewed by pressing the Update button. Onceyou are satisfied with the selected parameters, the Summary Table can be saved as an excel
spreadsheet by clicking on save from the top left hand menu shown in Figure 2.5.5.

Figure 2.5.5 Save Menu
A Save Summary Table dialogue box will appear (Figure 2.5.6) to allow you to name and save as an
excel spreadsheet (*.xld).

Figure 2.5.6 Summary Table Save As Option
The Summary Table is also added to the Database Window as a Summary Table Tab. Additional
summaries can be created and a tab will be added to the Dataset for each Summary Table. The
Summary Table Tabs in the Dataset will be numbered in the order they were created as shown in
Figure 2.5.7.

Figure 2.5.7 Database Window Summary Tab

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2.5.2 Data: Decode Database(s)When a Dataset is open and selected, clicking on Decode Database(s) from the Data Menu displays
a dialogue box asking to re-enter the password for the Dataset.

Figure 2.5.8 Re-enter Password
A warning message will be received if the database has already been decoded. You can choose to
overwrite existing decode as seen in Figure 2.5.9. Selecting No will send you back to the original
Dataset.

Figure 2.5.9 Decode Database Error Message
Once the password is entered the Dataset will be copied and ‘_DECODED’ will added to the file name.
Edit Dose IDs
The ID Decoder Dialogue Box is then opened allowing you to Edit Dose IDs and Add Dose IDs. The
Clear All and Delete Last buttons can be used to during the selection process

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Figure 2.5.10 ID Decoder
If Edit Dose IDs is needed, it must be performed before the Add Dose ID function. If not, an error
message will be received stating that this action will invalidate any Dose IDs already assigned.
The Edit Slide IDs dialogue box list the Slide Names on the left and any changes made on the right(Figure 2.5.11). To change a slide id, highlight the desired slide and press the Change button. Press
Cancel at any time to exit Edit Slide IDs.

Figure 2.5.11 Edit Slide ID
The Update IDs dialogue box will appear and allow any necessary changes to be made. Oncechanges are made press OK (Figure 2.5.12).

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Figure 2.5.12 Update Slide IDs
Once changes are complete the Edit Slide IDs Dialogue box will re-appear and show any changes
made (Figure 2.5.11).
Once complete, press the OK (2.5.10) will once again appear.
Add Dose IDs
The ID Decoder Dialogue Box (Figure Now you are ready to Add Dose IDs.
After pressing the Add Dose IDs button the Create New Dose ID dialogue box will appear and allow
you to select the Dose ID (Figure 2.5.13). The three options are to type in the name and units, Positive
Control or Negative Control. The Drop down list for units will remember the last entry and continue togive that entry to you as an option. If no entries are present in the drop down box, you can simply typein the desired units. Press OK.

Figure 2.5.13 Create New Dose ID
The Assign IDs dialogue box will appear and allow you to select the slides to add to dose group. Once
all slides are selected, press OK.

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Figure 2.5.14 Assign IDs
Continue adding dose groups and assigning slides using the Add Dose IDs button on the ID Decoder
Window (Figure 2.5.15). The Dose ID and slides assigned to that dose will appear in the window as
the doses are added. Remember, the Clear All and Delete Last buttons can be used wheneverneeded.

Figure 2.5.15 ID Decoder with Dose IDs Assigned
After all doses are added, press OK. All slides must be assigned to a dose group before proceeding.

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Figure 2.5.16 Database Window Decode Tab
A Tab will then appear in the Database Window containing all the information entered as seen in
Figure 2.5.16.

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2.5.3 Data: View Outliers

When a database is open and selected, clicking View Outliers from the Data Menu displays a SelectRequired Parameter dialogue box (Figure 2.5.17).

Figure 2.5.17 Select Required Parameters for Outliers
Select a parameter from the dropdown list to view and press OK. If the Dataset is decoded, a dialogue
box will appear allowing you to select the dose groups to be included as shown in Figure 2.5.18. If theDataset is not decoded, a list of slide ids will be listed in the dialogue box. Selected dose groups or
slide ids will have their checkboxes labelled with a tick. Select All and Deselect All buttons can be
used.

Figure 2.5.18 Select Dose Groups for View Outliers
Press OK.
Any outliers in that selected parameter will be shown in the View Outlier Window as shown in Figure
2.5.19.

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Figure 2.5.19 View Outlier Window
The upper pane of the Outliers Window shows the ID, Session, any Notes, the Name of the image,and all analysis parameters. When you click on a row of data, the image from which the data was
obtained is displayed in the lower pane of the window along with a calibrated ruler to show comet
lengths.

2.5.4 File Menu for View Outliers
When the View Outlier Window is open, the file options change (Figure 2.5.20).

Figure 2.5.20 View Outlier Menu Bar

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Database Viewer

The View Outliers option automatically shows all outliers within three standard deviations of the mean.
Under the Exclusion Criterion drop down menu, you have the option of selecting outliers within two
standard deviations of the mean (2 SD) or three standard deviations of the mean (3 SD). If you chose
two standard deviations from the mean, the View Outlier Window will automatically update. You canalso change which parameter to view by selecting a different parameter from the list (Figure 2.5.20).

2.5.5 Exclude Data

Figure 2.5.21 View Outlier Menu Bar
If you want to Exclude Outlier Data, select Exclude Data from the file menu. An Exclude Data
Dialogue box will appear as seen in Figure 2.5.21.

Figure 2.5.22 Exclude Data
Selecting No will return you to the view outlier window. Selecting Yes will exclude the data and theData Tab, Data Audit Tab and Session Record Tab will show the excluded data as seen in Figures
2.5.22, 2.5.23, and 2.5.24.

Figure 2.5.23 Excluded Data in Data Tab

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Figure 2.5.24 Excluded Data in Data Audit Tab

Figure 2.5.25 Excluded Data in Session Record Tab

2.5.6 Show Database

Figure 2.5.26 View Outlier Menu Bar
Show Database puts the Database Window on top of all the other windows.

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2.6 DBV Tab: Windows

Figure 2.6.1 The Windows Tab

2.6.1 Windows: Tile

This determines how the open Datasets in the Database Viewer will be displayed. Selecting Tile willallow the user to see all open datasets in one window.

2.6.2 Windows: Cascade

This determines how the open Datasets in the Database Viewer will be displayed. Selecting Cascade
will show the selected Dataset in front of all other Datasets. The Cascade option is also the default.

2.7 DBV Menu: Help

Figure 2.7.1 The Help Menu

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2.7.1 Help: Help

Selecting Help opens the Software Guide for the Database Viewer. Note that Adobe Reader or similarsoftware is required to view the Software Guide.

2.7.2 Help: About

Selecting About displays information about the version number and release date of the DBV, gives
copyright credits and contact information.

Figure 2.7.3 The About Dialogue Box

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SECTION 3: INSTALLING THE SOFTWARE
Download: my.andor.com
Contact: www.andor.com/contact_us/support_request

To install the Database Viewer from the Installation CD, simply insert the CD into the drive and follow
instructions. Or if the CD does not auto play, then select the Start.exe program from the root folder of
the CD.
If running a standalone CD made by Komet®, Komet GLP or DBV, then just insert the CD and DBV
will start and load the default Dataset. If the CD does not Auto run, then double click on the Autorun.ini
file in the CD root folder.

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SECTION 4: 4 DEFINITIONS AND INFORMATION
ON DECODING DATASETS AND CREATINGSUMMARY TABLES
Data Summary Creation as a Preliminary to Statistical Analysis in The GLP Database Viewer Definitions
According to a recent paper on monitoring genotoxic effects in humans presented (Albertini RJ et al),the statistical analysis of data from genetic toxicology assays follows two distinct approaches,
depending on whether the data is continuous or binary. The former data is produced by assays suchas comet and UDS, where features of interest are respectively %DNA damage and number or area ofdeveloped silver grains, driven by DNA synthesis. The latter is represented by assays such as
micronucleus (MN) or Chromosome aberration, where we are concerned with presence or absence of
micronuclei or aberrations in various classes. The latter data generally follows a binomial distribution,
while the former is commonly normal or normal after transformation. The techniques utilized in data
analysis make no assumptions about the underlying form of the distribution, simply the nature of thedata.
In this summary we will consider only the continuous forms in relation to the data summary functions
within the Database Viewer.
•First of all the Study Director chooses the study design depending on the scientific questions
being asked. This will establish the dataset created during scoring and will include the numberof samples, number of replicates (slides) per sample. The set of sample replicates will generally
be considered the unit of exposure. This is determined in Komet protocol set up. Scoring willcommonly be carried out blind to minimize the potential for scorer bias, but as scoring proceeds
Komet prompts the scorer to introduce replicate samples sequentially and pools the data for asample from the set of replicates. For the purposes of a concise process definition, we will referto the ith unit of exposure ui(e).

•Next the dataset will be decoded in the Database Viewer. Using the Decoder tool, samples aregrouped into dose or exposure groups or other groupings key to the nature of data analysis.
Examples include comparisons of datasets from replicate experiments or the study ofunderlying variability in positive or negative control data from a series of datasets. For the
purposes of a concise process definition, we will call the ith dose or exposure group gi(e).

•The next step is to specify the parameters to be used for the data summaries and these include
selections from mean, standard deviation, standard error, dispersion and coefficient of variation.
Alternatively, we can choose a non-parametric description in the form of percentile, which
includes the median (50 percentile). These parameters are then computed row-wise andpresented for each unit of exposure and column-wise for each dose or exposure group. The
computations for groups is based on computing mean of means or mean of percentiles and thestandard deviation etc. is computed on the variability of means or medians.

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This is presented in mathematical notation below.

U(e)
U1(e)
U2(e)
U3(e)
U4(e)
U5(e)
Group, G1
Ã(µ) or Ã(P)Á(µ) or Á(P)H(µ) or H(P)CV(µ) orCV(P)
Number, n

Mean
µ1
µ2
µ3
µ4
µ5
µ1(µ)
Ã1(µ)
Á1(µ)
H1(µ)
CV1(µ)

U6e)
U7e)
U8(e)
U9(e)
U10(e)
Group, G2
Ã(µ) or Ã(P)Á(µ) or Á(P)H(µ) or H(P)CV(µ) orCV(P)
Number, n

µ6
µ7
µ8
µ9
µ10
µ2(µ)
Ã2(µ)
Á2(µ)
H2(µ)
CV2(µ)

percentile
P1
P2
P3
P4
P5
µ1(P)
Ã1(P)
Á1(P)
H1(P)
CV1(P)

Std Dev
Ã1
Ã2
Ã3
Ã4
Ã5

Sem
Á1
Á2
Á3
Á4
Á5

Dispersion
H1
H2
H3
H4
H5

CV
cv1
Cv2
Cv3
Cv4
Cv5

n
e.g.100
N2
N3
N4
N5

P6
P7
P8
P9
P10
µ2(P)
Ã2(P)
Á2(P)
H2(P)
CV2(P)

Ã6
Ã7
Ã8
Ã9
Ã10

Á6
Á7
Á8
Á9
Á10

H6
H7
H8
H9
H10

Cv6
Cv7
Cv8
Cv9
Cv10

N6
N7
N8
N9
N10

e.g. 5e.g. 5

Table 1. Data Summary Table definition for the GLP Database Viewer

References
Richard J. Albertini, Diana Anderson, George R. Douglas, Lars Hagmar,
Kari Hemminki, Franco Merlo, A.T. Natarajan, Hannu Norppa, David E.G. Shuker, Raymond Tice,
Michael D. Waters, Antero Aitio. “IPCS guidelines for the monitoring of genotoxic effects ofcarcinogens in humans” Mutation Research 463 2000 111–172

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