Med Associates Product Manual · Med Associates, Inc. CHAPTER 2 GETTING STARTED Software Installation If the computer was purchased as part of Activity Monitor system froanm Med Associates,

instrumentation and software for research

ACTIVITY MONITOR SOF-812 USER’S MANUAL

DOC-101 Rev. 1.3 Copyright ©2015 All Rights Reserved

Med Associates Inc. P.O. Box 319 St. Albans, Vermont 05478

Phone: 802.527.2343 Fax: 802.527.5095 www.med-associates.com

MED A S SOCI ATES I NC. SOF-812 ACTIVITY MONITOR

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DOC-101 Rev 1.3 Copyright © 2015 Med Associates, Inc.

notes

http://www.razelscientific.com/


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Table of Contents

Chapter 1 Introduction ................................................................................................... 1

Key Terms ...................................................................................................................................... 1

Defining Distance Traveled .......................................................................................................... 2

Defining Ambulatory Trigger ....................................................................................................... 3

Differentiating Between Large/Quick and Small/Slow Movements........................................ 3

Chapter 2 Getting Started .............................................................................................. 5

Software Installation ..................................................................................................................... 5

Hardware Setup ............................................................................................................................. 5

Modifying IR Array Height ........................................................................................................... 5

Chapter 3 Hardware Configuration .............................................................................. 6

Setting Chamber Properties ......................................................................................................... 7

Advanced Test ............................................................................................................................... 9

Chapter 4 Acquiring Data ............................................................................................. 11

Create a New Project .................................................................................................................. 11

Create a Protocol ......................................................................................................................... 12

Start Collecting Data ................................................................................................................... 12

Chapter 5 Data Analysis................................................................................................ 16

Analysis Settings ......................................................................................................................... 16

Zone Settings ............................................................................................................................... 17

Analyze the Data ......................................................................................................................... 19

Filter Sessions .............................................................................................................................. 20

Analysis Range............................................................................................................................. 21

Select Columns Button ............................................................................................................... 21

Chapter 6 Menu Options ............................................................................................... 24

File Menu Options ....................................................................................................................... 24

View Menu Options ..................................................................................................................... 26

Project Menu Options ................................................................................................................. 26

Help Menu Options ..................................................................................................................... 27

Chapter 7 Session Maintenance .................................................................................. 28



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Chapter 8 Inserts for Open-Field Activity ................................................................. 29

Hole Board Task Floor ................................................................................................................ 29

References Cited: ........................................................................................................................ 30

Dark Box Insert (Light/Dark Test) ............................................................................................ 31

Two Chamber Place Preference ................................................................................................ 32

Chapter 9 Start on Remote Start Command ............................................................ 33

Chapter 10 File Naming and Types ............................................................................ 34

File Types ..................................................................................................................................... 34

File Naming .................................................................................................................................. 34

Chapter 11 Legacy Data File Formats ........................................................................ 35

Summary Data ............................................................................................................................. 35

Analyzed Data .............................................................................................................................. 36

Hole Board Task Data ................................................................................................................. 36

Exported Raw Data Files ............................................................................................................ 37

Appendix A Contact Information ............................................................................... 38


MED A S SOCI ATES I NC. SO F-8 12 ACT IV ITY MO NITO R

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CHAPTER 1 INTRODUCTION

Open Field Activity (OFA) Monitoring is a powerful assessment tool that quantifies distance traveled and stereotypic movements within the defined space of the Open Field Arena. Special inserts may be used with the system to perform hole board tasks, light/dark tests, and conditioned place preference protocols.

Key Terms

Figure 1-1 - Illustration of Ambulatory Count vs. Distance Traveled

Ambulatory Count: The ambulatory rectilinear distance traveled in beams. In Figure 1-1 the ambulatory count is represented by the blue line; there are 13 ambulatory counts.

Ambulatory Episode: Recorded when the number of ambulatory counts meets or exceeds the ambulatory trigger.

Ambulatory Movement: Movement is ambulatory when the subject leaves the square defined by the stereotypic box (see below).

Ambulatory Trigger: The minimum number of ambulatory counts for the current ambulatory movement to be considered an Ambulatory Episode. See Defining Ambulatory Trigger, page 3.

Average Speed: The average speed in cm/s of all ambulatory episodes.

Distance Traveled: The total Euclidean distance of all ambulatory episodes in centimeters. In Figure 1-1 the Distance Traveled is indicated by the black line. See Defining Distance Traveled, page 2.

Jump Counts: Number of time periods that no X or Y-axis beam breaks were detected. This primarily occurs when the animal jumps, or on rare occasions, when the animal is rearing and the IR (infrared) beams fail to contact their body.



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Jump Time: The total duration in seconds of the jump counts.

Stereotypic Box: A user-defined square whose size is measured in beams. Movements outside this box are ambulatory.

Resting Delay: An ambulatory episode ends when the subject stays inside the stereotypic box for the duration of the resting delay. Resting Delay is expressed in seconds.

Stereotypic Count: The rectilinear distance, in beams, traveled while inside the stereotypic box.

Stereotypic Movements: Movements recorded while the subject stays inside the stereotypic box.

Vertical Counts: Number of times that the animal rears. Rearing is defined as concurrent beam breaks in the Z-axis and X or Y-axes.

Vertical Time: The total duration in seconds of the vertical counts.

Defining Distance Traveled

In Figure 1-2 below, the black dots represent IR (infrared) beams and each grid square represents half the distance between IR beams (the software resolution). The stereotypic box is indicated by the large blue box (see Key Terms). The subject’s position at time zero is represented by the blue dot (X), and each black arrow with a corresponding number represents a subject movement. Therefore, the subject made three movements within the stereotypic box and four outside.

Figure 1-2 – Distance Traveled Diagram

At time zero, Activity Monitor centers the box on the subject. If the subject moves outside the box, the movement is considered ambulatory and the box re-centers on the subject. The movement to position 4 represents a transition to ambulatory movement and the dashed blue box represents the re-centered box. If the subject remains inside the re-centered box for longer than the Resting Delay, the subject becomes stereotypic. However, in this example the subject moves to position 7 before the Resting Delay expires and remains ambulatory.



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The Distance Traveled measure is the ambulatory distance traveled. In the example above the Distance Traveled is represented by the purple dashed line.

Distance Traveled is modified if Include Minor Waypoints is activated. If Include Minor Waypoints is activated, Distance Traveled is the sum of all ambulatory movements. So, in the example above, the Distance Traveled would be the distance from X to 4, plus 4 to 5, plus 5 to 6, plus 6 to 7.

Include Minor Waypoints increases Distance Traveled 8% on average; but differences of 3% to 15% have been observed. Include Minor Waypoints is useful when comparing activity data with other systems not using a Distance Traveled filter.

Defining Ambulatory Trigger

The Ambulatory Count is the distance traveled in beams and is represented below by a thick purple line in Figure 1-3. In this example the Ambulatory Count is 6.

The Ambulatory Trigger is the minimum number of ambulatory counts for the current ambulatory movement to be considered an Ambulatory Episode. Therefore, if the Ambulatory Trigger is set to 6 or lower, the movement will be considered an Ambulatory Episode and an ambulatory episode speed will be calculated.

Figure 1-3 – Ambulatory Count Diagram

Differentiating Between Large/Quick and Small/Slow Movements

With the stereotypic box size, resting delay, and ambulatory trigger items described above, it is possible to differentiate groups of subjects based upon their types of movements using ambulatory time, ambulatory counts, ambulatory episodes, average speed, and distance traveled.

Assume there are two groups of subjects, a control group (C) and a loco-motor impaired group (P). The loco-motor impaired group is a Parkinsonian animal model. If the distances traveled for the two groups were measured, Cs may move 1000 cm in 20 minutes with periods of quick movements (high speed) and periods of minimal movements (resting or stereotypic). For the same time period, Ps may



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also move 1000 cm but with few, if any, fast movements and continuous slow movements. Therefore, distance traveled may not accurately depict between-group differences in loco-motor activity.

The stereotypic box size and the resting delay combine to create a threshold whereby a subject must move a certain distance (stereotypic box size) in a maximum amount of time (resting delay) to maintain its ambulatory status. By determining a stereotypic box size large enough for Cs to leave in an amount of time (resting delay) that Ps cannot, the user may be able to differentiate the groups by analyzing for ambulatory times and counts.



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CHAPTER 2 GETTING STARTED

Software Instal lation

If the computer was purchased as part of an Activity Monitor system from Med Associates, the driver and software installation was completed at the factory. If the computer was not purchased from Med Associates or was not a part of the system, follow the instructions below to install the drivers and software. Before beginning the software installation, phone, fax or e-mail Med Associates with the registration information in order to receive the software installation password. This password will be necessary during the software installation process. Insert the Activity Monitor CD into the CD drive and at the welcome screen click Install. If the CD does not auto-start, navigate to the CD drive in Windows Explorer and double click “autorun.exe” and click Install at the welcome screen. Successful installation of each component will be indicated by a green check mark, a red X will indicate an unsuccessful installation. When prompted enter the user name, company name and software installation password. When the installation completes, click Finish.

Hardware Setup

Refer to the USB Open Field Activity Wiring Guide, DOC-297, for hardware setup instructions.

Modifying IR Array Height

The subject’s location and motion are tracked by three pairs of infrared (IR) strips (arrays) mounted to the sides of the chamber. There is one pair of strips for each of the X, Y and Z-axes. A pair of strips consists of one strip of IR emitting LEDs, and one strip of IR detectors.

Do not assume that the factory set IR array heights are appropriate for the experiments being conducted. Different ages and strains of subjects may have different physical characteristics necessitating IR strip height adjustments. The use of inserts (Chapter 8) may also require the IR strips to be adjusted. The closer the IR array strips are located to the subject’s vertical center (for X & Y-arrays), the better the results will be. If a subject is too low for the IR strips, or capable of crouching periodically below the strips, the subject may disappear from sight of the system from time to time. The software is designed to remember the subject’s last location and pick back up when the subject becomes visible again. Typically, this will have little bearing on the data; however, if using speed data, there could be a sudden increase in a subject’s speed and Jump Counts and Jump Time will be affected. There may be other scenarios whereby inaccurate IR strip placement may present erroneous data, so use care in this process. The Z-axis IR array strips should be placed above the X & Y-axes in the lowest position capable of detecting vertical activity and not detecting normal X & Y activity. If the strips are too high, some rearings may not be detected, or slight bouncing while rearing may cause multiple rearings to be detected when only one rearing episode was indeed elicited.



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CHAPTER 3 HARDWARE CONFIGURATION Start Activity Monitor via the Start menu or by double clicking the desktop icon and select File > Configure Hardware to open the hardware configuration screen. The screen will display currently connected devices and devices that were previously connected.

Figure 3-1 - Configure Hardware Screen

Table 3-1 - ENV-520 Properties

Item Description

Detect Detects all connected ENV-520 devices. Press to refresh the device list.

Advanced Test Displays the screens shown in Figure 3-5 & Figure 3-6, which displays the X, Y, Z-axes data from the ENV-520 devices. Each device must be configured before Advanced Test can be used.

Configure Displays the configuration screen, Figure 3-3, for the currently selected devices. Select the chamber type, acquisition rate, and hole board configuration.



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Test Tests the currently selected devices. This updates the corresponding Connected and Status fields.

Remove Deletes the currently selected device from the list of available devices.

Reset Names Resets the names of the currently selected devices to their node number.

OK Applies the changes and closes the configuration screen.

Cancel Discards changes and closes the configuration screen.

Apply Applies the changes.

Node The node number of the ENV-520 device. ENV-520 USB devices are prefixed by “USB”. ENV-520 devices connected to a DIG-729 are prefixed by the DIG-729 index number (typically “0”).

Name The name of the ENV-520 device. The name can be changed by double-clicking in the cell and entering a new name. The chamber name will be shown and referenced during the data acquisition process.

Connected Displays whether or not the device is connected to the computer (Yes, No).

Status Displays the status of the device (OK, Failed).

Type Displays the chamber type. Possible chamber types are "Not Configured"

"ENV-510 - 28cm x 28cm"

"ENV-515 - 43cm x 43cm"

"ENV-515-32 - Dual ENV-520 43cm x 43cm"

"ENV-515X-16 - 81cm x 81cm"

"ENV-515X-32 - Dual ENV-520 81cm x 81cm" Select a device using the checkbox and click the Configure button to set the type.

Samples Per Second

The acquisition rate of the ENV-520 device. Typically this is 20 samples per second, which is equal to a 50 millisecond resolution.

Hole Board Installed

Whether a hole board activity floor is installed in the respective chamber (Yes, No).

Hole Board Strips Installed

Whether hole board IR strips are installed in the respective chamber (Yes, No).

Setting Chamber Properties

Select a chamber to be configured by ticking the checkbox, Figure 3-2, or select multiple chambers to apply the same settings to all selected chambers. Click Configure to open the Configure Chambers window, Figure 3-3.

In the Configure Chambers screen set the chamber type with the Type dropdown, change the Samples Per Second (if desired) and check the Hole Board Installed checkbox if the hole board activity floor is being used. Use the Device drop down to apply the settings to the selected chamber or all chambers being used. Click Apply



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and OK to apply the settings and return to the ENV-520 Devices Properties screen. Notice the screen has been updated to reflect the configuration settings, Figure 3-4.

Figure 3-2 – ENV-520 Devices Properties Screen

Figure 3-3 - Configure Chambers Screen

Figure 3-4 - Updated Device Properties



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Advanced Test

The advanced test simultaneously tests all configured ENV-520 devices. A table view showing the raw data from all chambers can be displayed, Figure 3-5, or a mixed view with the table and a visual display of the currently selected chamber can be chosen, Figure 3-6.

Figure 3-5 - Advanced Test Table View

Table 3-2 - Advanced Test Items

Item Description

Device The name of the ENV-520 device.

Tick Count

The number of ticks received from the device. Each device increments a tick counter at the specified acquisition rate. By default the tick counter will increase by 20 ticks/second.

X / Y / Z The axis name. The X-axis corresponds to IR pair 1, the Y-axis corresponds to IR pair 2, and the Z-axis corresponds to IR pair 3.

(Low) The raw value received from the lower half of the corresponding axis. Used by Med Associates Technical support for diagnostics.

(High) The raw value received from the upper half of the corresponding axis. Used by Med Associates Technical support for diagnostics.

(Breaks) The number of beam breaks that have occurred so far on the specified axis and device. This is useful in determining if a beam flicker error is present. A beam flicker error occurs when a beam break is recorded, yet nothing has physically broken the beam.



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Figure 3-6 - Advanced Test Mixed View



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CHAPTER 4 ACQUIRING DATA Once the hardware configuration is complete, Activity Monitor requires only two pieces of information to begin collecting data: a project name and a protocol. All analysis settings may be established post-hoc.

Create a New Project

From the Activity Monitor main screen (Figure 4-1) select New Project… or select File > New > Project to open the Save As window. Supply a project name and save location and click Create.

Once the new project is created the project home screen will appear (Figure 4-2).

Figure 4-1 - Activity Monitor Home Screen

Figure 4-2 - Project Home Screen



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Create a Protocol

On the Project Home Screen click New Protocol… or click File > New > Protocol to open the Protocol Settings screen (Figure 4-3). The duration in minutes is the only required setting unless a hole board task is being run. If a hole board is to be used see Chapter 8, Inserts for Open-Field Activity.

Figure 4-3 - Protocol Settings Screen

Enter the required duration, click OK, provide a name for the protocol and click OK to save the protocol and return to the Project Home Screen.

Start Collecting Data

From the Project Home Screen click Acquire Data… or click Project > Acquire Data to open the Acquire Data Screen (Figure 4-4). Click in the Subject box to enter the subject’s name (enter Group name and a comment if desired) and click the Start button. The Waiting For Animal Entry screen depicted in Figure 4-5 will appear and data collection will begin* when the test subject is placed in the chamber.



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Figure 4-4 - Acquire Data Screen

* Additional triggering options are configurable on the Preferences screen. See Chapter 6, Table 6-1.

Figure 4-5 - Waiting for Animal Entry



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During the experiment the data acquisition screen, presented below, will display the subject’s path and the stereotypic box if selected.

Figure 4-6 - Data Acquisition Screen During Data Collection



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The lower portion outlined in red above displays the results as they are being collected. Use the scroll bars to view all of the available data.

As the experiment is running, use the Acquisition menu to Stop, Pause and Resume data collection as needed. The screen will change color when data collection is complete.

Following data acquisition the most common actions are:

- Analyze the data: click Project > Analyze Data

- Acquire more data: click Acquisition > Acquire Data…

- Return to the Home Screen: click Acquisition > Close Data Acquisition



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CHAPTER 5 DATA ANALYSIS Activity Monitor’s default analysis settings are appropriate for the majority of protocols. The settings most commonly changed from their default values are the data bin settings.

Analysis Settings

On the Project Home screen click New Analysis Settings… or File > New > Analysis Settings to open the Analysis Settings screen seen in Figure 5-1.

Figure 5-1 - Analysis Settings Screen

The default setting of 4 beams for the Stereotypic Box is recommended. If a rat-sized chamber is being used with mice, a value of 2 or 3 may be appropriate.

If pups or other non-standard sized animals are being used, some experimentation with the Stereotypic Box size may be required. If the Analysis Settings are not ideal during acquisition, they may be changed during data analysis.

Table 5-1 - Analysis Settings

Item Description Stereotypic Box A user-defined square whose size is measured in beams. Movements outside this box

are ambulatory. Ambulatory Trigger The minimum number of ambulatory counts for the current ambulatory movement to

be considered an Ambulatory Episode. Resting Delay An ambulatory episode ends when the subject stays inside the stereotypic box for the

duration of the resting delay. Include Minor Waypoints

Removes filtering from the Distance Traveled measure. Filtering removes spurious distance measurements that may occur from tail flicker, etc. It is recommended that this option be left off unless trying to match results with a system that doesn’t have a Distance Traveled filter. See Defining Distance Traveled, pg. 2.

Binning - By Duration Analyzes the data in blocks of specified duration. Binning - By Segments The analyzed data block duration is derived by dividing the protocol duration by the

number of segments entered. Save As Saves the analysis settings with the specified name. OK Closes and saves the analysis settings. Cancel Exits the analysis settings screen without saving.



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Zone Settings

Click New Zone Settings… on the Project Home screen or click File > New > Zone Settings to open the Zone Settings screen. Figure 5-2 shows an example of the Zone Settings screen with one zone. Zones are editable and may be dragged to a new location or resized. Click and drag with the mouse to move a zone or click and drag an edge or corner of a zone to resize it. Zones cannot overlap each other.

The Pre-Defined Zones drop down box offers a selection of commonly used zone settings. Perhaps the most useful is a single zone in the center. This produces a remainder zone which is conducive to thigmotaxic analysis.

To edit a zone name click in the corresponding text field in the Zone Name column and type the desired zone name.

Once the zones are established click OK to save the zone settings and return to the Project Home screen.

Figure 5-2 - Zone Settings Screen

Note: The pre-defined zone coordinates differ slightly between Activity Monitor 7 and prior versions of Activity Monitor. To properly compare data analyzed with Activity Monitor 6 (or prior) with data analyzed with Activity Monitor 7, import the earlier data and re-analyze using the same zone analysis settings. Alternatively, create a set of Activity Monitor 7 zone coordinates to effectively match the prior version’s zone coordinates. The prior version’s zone settings are listed in the zone analysis file generated when the zone analysis is performed. The file name will be similar to “subject_group_experiment.Zone”.



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Table 5-2 - Zone Settings

Item Description

New Zone Inserts a new zone with a semi-random location and color.

ENV-510/ENV-515 Scales the axes labels to the specified chamber type. The dropdown control will only list chamber types of currently configured chambers.

Pre-Defined Zones Opens a dropdown list of commonly used zone settings to choose from.

Beam An axis label displaying specific beam numbers.

Thumbnail An iconic representation of each zone.

Location & Size The top-left corner of the zone specified in beams (X, Y); relative to the origin (0, 0) at the bottom left corner. The width and height of the zone in beams and centimeters.

Zone Name The name of the zone. This field is editable.

Remove When a zone's check box is selected, the remove button is enabled and the selected zone(s) may be deleted. The remainder zone cannot be deleted.

Save As Saves the zone settings with the specified name.

OK Closes and saves the zone settings.

Cancel Exits the Zone Settings screen without saving.



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Analyze the Data

Once the analysis and zone settings are established click Analyze Data… on the Project Home screen or Project > Analyze Data from the menu bar to open the Analyze Data screen in Figure 5-3.

Figure 5-3 - Analyze Data Screen

Table 5-3 - Analyze Data Options

Item Description

Analysis Settings Selects the analysis settings used to analyze the data.

Zone Settings Selects the zone settings (if established) used to analyze the data.

Filter Sessions Allows filtering of the analyzed sessions shown in the lower portion of the screen. Sessions can be filtered by Start Date, Subject, Protocol, Group, or Session number.

Session Range Selects the time range to analyze the data.

Show Incomplete Sessions

Lists sessions that have a duration less than the associated protocol duration.

Select Columns Displays the Select Columns screen (Figure 5-7) which customizes the result columns displayed in the bottom portion of the Analyze Data screen.



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File Format Dropdown Displays the list of available output formats.

Output Target Dropdown

Displays the list of available actions, and if the action has a program associated with it, the program name is listed instead of the action. For example, Excel is typically associated with spreadsheet files, so “Excel” is listed as the output and “Spreadsheet” is chosen for the File Format.

Open Outputs the results in the selected format with the selected action.

Display Session Details Displays the session results of the selected row in a consolidated view, see Figure 5-8.

Display Path Displays the path for the selected animal, see Figure 5-9.

Use the Analysis Settings and Zone Settings dropdown selection boxes to select the analysis parameters applied to the sessions.

Fi lter Sessions

When the Analyze Data screen opens, no filters are applied, and all sessions are displayed in the results grid at the bottom of the screen. The Filter Sessions tool is used to narrow the set of sessions displayed. The filter options are: <No Filter>, Start Date, Subject, Protocol, Group, and Session Number. The filters may be applied to a depth of four levels. Each selected filter option will produce an associated column to the right of the Filter Sessions tree from which the desired selections are made. Filter Sessions Example: Select Protocol as the primary filter option to list all protocols in the first filter column. Marking a protocol as checked will display sessions from that protocol in the results grid. See the red arrow in Figure 5-4.

Figure 5-4 - Selected Protocol

Figure 5-5 - Click the X to Clear Selections

The secondary filter option will display all applicable items from the checked primary filter (Protocol). Select Start Date as the secondary filter option to display all start dates from the previously filtered items.



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Click the”X” (see red arrow in Figure 5-5) above a filter list to clear all filters in that list and remove all subsequent cascaded filters. The numbers below each filter list represent the number of items in the filtered list (before the slash) and the number of these items in the project as a whole (after the slash). For example, 1/5 Start Dates in Figure 5-5 above indicates the project’s sessions occurred on five separate days, and one day’s sessions meets the criteria of using the “Badger Protoco3” protocol. Manually stopping a session (Acquisition > Stop) yields an Incomplete Session. The “Show Incomplete Sessions” checkbox (Figure 5-3) enables these prematurely ended sessions to be displayed.

Analysis Range

Figure 5-6 - Analysis Range Selection

To analyze a specific time range of acquired data, use the Analysis Range fields “Start Time” and “End Time”. By default the Start Time is set to Begin, and the End Time is set to End, which will analyze the entire time range of the data. To view a limited time range, for example to view only the first two minutes of data, set the Start Time to Begin, and the End Time to 2 Minutes. To view the last two minutes of data, set the Start Time to protocol duration minus two minutes (for a 30 minute protocol, set the Start Time to 28 minutes), and set the End Time to End.

Select Columns Button

Click the Select Columns button to show the Select Columns dialog (Figure 5-7). Use this dialog to customize the result columns displayed in the results grid section of the Analyze Data screen (Figure 5-3). In the Results section of the Select Columns window, the Hole Board tab displays result columns relevant to hole board protocols. The Time Bin & Zone tab displays data results that are relevant to time bins, zones, or both. Setting the Time Bin radio button enables result fields applicable to time bins, and disables fields that only apply to zones. Setting the Zone radio button enables result fields applicable to zones, and disables fields that only apply to time bins. Use the Time Bins & Zone button to enable all result fields. The Settings section contains the General tab which displays columns applicable to the session; the values in these fields are not affected by changes on the Analyze Data screen. Analysis columns are listed under the Analysis tab, the values are dependent upon the analysis settings. The filtered and analyzed data are displayed immediately in the data grids in the lower portion of the screen. At this point the data can be viewed or saved to a file based on the choices made in the File Format (labeled “Spreadsheet” in Figure 5-3) and Output Target (labeled “Excel” in Figure 5-3) dropdowns.



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Figure 5-7 - Select Columns



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Figure 5-8 - Display Session Details

Figure 5-9 - Display Path Example



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CHAPTER 6 MENU OPTIONS

Fi le Menu Options

New

New Project – Creates a new project in the specified location and opens it.

New Protocol – Opens the protocol settings screen.

New Analysis Settings – Opens the analysis settings screen.

New Zone Settings – Opens the zone settings screen.

Open

Open Project – Opens an existing project.

Open Protocol – Displays a list of existing protocols.

Open Analysis Settings – Displays a list of existing analysis settings.

Open Zone Settings – Displays a list of existing zone settings.

Close Project

Closes the currently open project and returns to the Activity Monitor Project Selection Screen.

Preferences

Figure 6-1- Preferences Screen



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Table 6-1 - Preferences

Item Description

Automatically Open Last Project

At program launch Activity Monitor will automatically open the most recently used project, skipping the Activity Monitor Project Selection Screen.

Generate Summary File

Creates an ASCII text summary file that will be automatically saved in the same directory as the project. The file name is automatically generated from the values entered into the Subject, Experiment, and Group fields on the Acquire Data screen. The file will have the extension .Summary. This option allows the user to store to disk the summary data, which may also be printed, for backup. Every time a subject is run, the new summary data are appended to the existing .Summary file. See also Chapter 10.

Include Minor Waypoints

Removes filtering from the Distance Traveled measure. Filtering removes spurious distance measurements that may occur from tail flicker, etc. It is recommended that this option be left off unless trying to match results with a system that doesn’t have a distance traveled filter.

Start On Animal Entry

Enables the system to begin a session as soon as the subject is placed into the chamber and the first sets of IRs have been broken. This feature works well for the hole board test and for starting sessions when the computer is in another room.

Start On Remote Start

Enables the system to begin a session as soon as the Remote Start Event for that chamber has been set. This allows third-party programs (like MED-PC ® IV) to remotely start the activity chambers. If both “Start on Animal Entry” and “Start on Remote Start” are checked, the chamber will not start until it has received a Remote Start Event and the animal is present in the chamber. For more information see the Remote Start command. See Chapter 9.

Time Zone Local Time Zone: Displays all dates and times using the computer’s current time zone setting. Fixed Time Zone: Displays all dates and times using the time zone selected from the drop down box on the Preferences Screen, see Figure 6-1.

Video Options Determines the algorithm used to create video files.

Legacy Options Relative Reporting Mode: Each time bin holds the sum of the data since the last time bin. Absolute Reporting Mode: Each time bin holds the sum of all data since the experiment began. The reporting mode affects how the data looks when it is sent to the printer and how the data looks in the summary data file. It is also used to determine how the data will be presented in the analyzed data files.



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Configure Hardware

Refer to Chapter 3 for hardware configuration.

Import

Imports raw data from previous versions of Activity Monitor into the currently opened project. Displays an open file dialog, which prompts for a .zip file. Raw data, protocols, and analysis settings are imported. Each protocol has an associated analysis setting. The name for each imported analysis setting is “_imported <protocol name>”.

Print

Prints the current screen.

Exit

Exits Activity Monitor.

View Menu Options

These options determine the appearance of the real-time activity graph display.

Graph Axes

Displays the X/Y axes and the appropriate units on the animal's graph.

Stereotypic Box

A user-defined square whose size is measured in beams. Movements outside this box are ambulatory.

Line Trace

Plots a dot as the center of the subject and draws a line showing all movement.

Project Menu Options

Acquire Data…

Opens the Acquire Data screen to begin data collection. See Chapter 4.

Analyze Data

Opens the Analyze Data screen. See Chapter 5.

Session Maintenance

Opens the project’s Session Maintenance screen. See Chapter 7.



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Help Menu Options

Software User’s Manual

Opens the Activity Monitor User’s Manual in .pdf format.

Wiring Guide (ENV-520USB)

Opens the Open Field Activity Wiring Guide for the ENV-520USB in .pdf format.

Legacy Wiring Guide (ENV-520)

Opens the Open Field Activity Wiring Guide for the ENV-520 in .pdf format.

About

Displays the Activity Monitor version information screen.



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CHAPTER 7 SESSION MAINTENANCE The Session Maintenance screen is accessed by clicking Project > Session Maintenance. This screen provides the ability to delete sessions and to modify a session’s chamber type. The changes on this screen are permanent. Once sessions are deleted they are permanently removed.

If a session was accidentally recorded with the wrong hardware configuration (for example, the hardware was configured as an ENV-510 mouse chamber when the session was actually run in an ENV-515 rat chamber), the hardware configuration can be modified. After the hardware configuration for a session has been changed, all analysis performed on that session will use the updated hardware configuration.

Figure 7-1 - Session Maintenance Screen

Table 7-1 - Session Maintenance Items

Item Description Filter Sessions Dropdown selections to filter data by start date, subject, protocol, group or session. Select Columns Opens window to select or deselect columns to be displayed. Modify Chamber Type

Opens window to change chamber type used.

Delete Deletes selected session row.



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CHAPTER 8 INSERTS FOR OPEN-FIELD ACTIVITY

Hole Board Task Floor

The Hole Board Task has been used for decades as a test for spatial orientation, working memory, exploratory behavior, and attention (Bert et al., 2009; Brown and Nemes 2008; Depoortere et al., 2010; Douma et al., 1998).

The hole board floor insert has 16 holes (four rows of four equidistant holes) with an underlying food tray. The X & Y-axes IR arrays must be attached to the chamber using the lowest available screw holes. This places the IR beams between the floor and the tray to detect entries into the holes. Food may be placed into the tray for learning and memory protocols using working and reference memory ratios. A second, non-reward application is to simply place the animal on the hole board insert and monitor hole entries for novelty/curiosity assessment. Typical reward associated paradigms involve habituation (pre-testing) protocols and non-habituation (no pre-testing) protocols.

To configure a hole board task floor protocol, create a new protocol and check the “Use Task Floor” checkbox on the Protocol Settings screen (Figure 8-1). Select task holes by clicking on the desired hole. Green holes are task holes, gray holes are non-task holes. Hole number 4 is closest to the ENV-520 controller. To automatically end the session when all green task holes have been entered at least once, check End Session on Task Completion.

Figure 8-1 - Hole Board Task Floor Settings

In order to run a hole board protocol, the animal chambers have to be configured with the hole board hardware. Refer to Chapter 3 and the USB Open Field Hardware Wiring Guide DOC-297, to configure the chambers with hole board hardware. Hole board protocols produce hole board specific data, defined below in Table 8-1. Hole board results are calculated when the session is complete, and are not available during data acquisition. Analyze the hole board session(s) to view hole board results. If hole board results are not visible, see Chapter 5 and refer to the section on selecting result columns (Figure 5-7).



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Table 8-1 - Hole Board Data File Values

Item Description

Latency to First Hole Time elapsed (seconds) between starting the session and entry into the first hole.

Novel Task Entries The number of task holes that were entered.

Novel NonTask Entries The number of non-task holes that were entered.

Novel Entries The number of holes (task and non-task) that were entered.

Repeat Task Entries The number of re-entries into task holes.

Repeat NonTask Entries The number of re-entries into non-task holes.

Repeat Entries The number of re-entries into holes (task and non-task).

Total Entries The total number of Novel and Repeat hole entries.

Mean Novel Task Interresponse Time (IRT) The mean time between novel task hole entries.

Mean Novel No-task IRT The mean time between novel non-task hole entries.

Mean Novel Total IRT The mean time between novel hole entries.

Working Memory Ratio Novel Task Entries divided by the total number of task entries.

Reference Memory Ratio Total number of task entries divided by the total number of hole entries.

Task Completion Time Time to enter all task holes at least once.

References Cited:

- Bert B, Voigt JP, Kusserow H, Theuring F, Rex A, Fink H. “Increasing the Number of 5-HT(1A)-Receptors in Cortex and Hippocampus Does Not Induce Mnemonic Deficits in Mice.” Pharmacology Biochemistry and Behavior 92(1) (2009 Mar): 76-81.

- Brown GR, Nemes C. “The Exploratory Behaviour of Rats in the Hole-Board Apparatus: Is Head-Dipping a Valid Measure of Neophilia?” Behavioural Processes 78(3) (2008 Jul):442-8.

- Depoortère R, Auclair AL, Bardin L, Colpaert FC, Vacher B, Newman-Tancredi A. “F15599, a Preferential Post-Synaptic 5-HT1A Receptor Agonist: Activity in Models of Cognition in Comparison With Reference 5-HT1A Receptor Agonists.” European Neuropsychopharmacology 20(9) (2010 Sep):641-54.

- Douma BR, Korte SM, Buwalda B, la Fleur SE, Bohus B, Luiten PG. “Repeated Blockade of Mineralocorticoid Receptors, but Not of Glucocorticoid Receptors Impairs Food Rewarded Spatial Learning.” Psychoneuroendocrinology 23(1) (1998 Jan):33-44.

- Additional examples of hole board protocols can be found by reviewing the following references.

- Duffy L, Cappas E, Scimone A, Schofield PR, Karl T. “Behavioral Profile of a Heterozygous Mutant Mouse Model for EGF-Like Domain Neuregulin 1.” Behavioral Neuroscience 122(4) (2008 Aug):748-59.

- Sargin D, El-Kordi A, Agarwal A, Müller M, Wojcik SM, Hassouna I, Sperling S, Nave KA, Ehrenreich H. “Expression of Constitutively Active Erythropoietin Receptor in Pyramidal Neurons of Cortex and Hippocampus Boosts Higher Cognitive Functions in Mice.” BMC Biology 9:27 (2011 Apr): 28. doi: 10.1186/1741-7007-9-27.



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- Shen EY, Ali SF, Meyer JS. “Chronic Administration of THC Prevents the Behavioral Effects of Intermittent Adolescent MDMA Administration and Attenuates MDMA-Induced Hyperthermia and Neurotoxicity in Rats.” Neuropharmacology 61(8) (2011 Dec):1183-92. doi: 10.1016/j.neuropharm.2011.07.002. Epub 2011 Jul 13.

Dark Box Insert (Light/Dark Test)

Figure 8-2 - Dark Box Insert for Open Field Activity

The two-compartment Light/Dark Test (Light/Dark Conflict Test) is a classic anxiety test and is easily incorporated into the system while examining other components of locomotor activity. The Dark Box Insert is opaque to visible light, but allows the IR beams to pass through. IR array height is the same as that for general open-field monitoring. The Dark Box is designed to cover half the area of the OFA chamber and has an opening that allows the subject to pass freely, but is sufficiently small to minimize the amount of light that enters the darkened area.

Place the Dark Box Insert in the activity chamber and then access the Zone Settings screen by clicking New Zone Settings … from the Project Home Screen or by clicking File > New > Zone Settings from the main menu bar. Match two zones with the two areas of the Light/Dark test, see Figure 8-3. The residual area may be placed between the two zones to minimize "bouncing" or "flickering" as a subject enters or leaves a zone and to examine time in transition between the two zones. Factory configured chambers are set up so that coordinate (0, 0) is at the opposite corner from the ENV-520 controller box and coordinate (16, 16) is in the same corner as the controller box.



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Figure 8-3 - Zone Analysis Settings for the Light/Dark Insert

Two Chamber Place Preference

Two Chamber Place Preference is used for conditioned place preference paradigms. The Two Chamber Place Preference Insert slides into the OFA chamber. After the box has been placed into the open-field environment the IR array heights will need to be adjusted to ensure subjects are tracked properly (see Modifying IR Array Height, pg. 5).

The insert covers the entire area of the chamber and is constructed of clear polycarbonate. Stickers, paper, or any easily removable material may be applied to the outside of these clear walls to provide distinct visual stimuli to maximize contextual differences. Do not cover the IR beams. Each side of the box has a different floor, grid rods and/or wire mesh. A manual guillotine door is provided that allows the subject to pass freely. Activity Monitor will automatically parse session data into zones and determine the amount of time the subject spends in each zone.



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CHAPTER 9 START ON REMOTE START COMMAND The Start on Remote Start option (Preferences window, Figure 6-1) enables the user to initialize the recording of data from the activity chamber with an external program such as MED-PC® IV. With this option selected, Activity Monitor will not start recording data until the remote start command arrives. To use Start on Remote Start, start the experiment as normal, then have MED-PC® IV send the remote start command at the appropriate time.

The remote start command is included in the file MPDEvents.dll. This file was installed on the computer when Activity Monitor was installed. The function used to issue the Remote Start/Stop commands are:

void StartActivityChamber(int Box); void StopActivityChamber(int Box);

The Box parameter is the chamber number to start (i.e. 1 – 16). Entering 0 as the Box number will start all of the chambers.

To issue the command from MED-PC® IV, include the file ACTIVITY.HED in the USER.PAS file. For example:

{Place $I Filename.HED files here.}

{$I ACTIVITY.HED}

Then from inside the program issue the StartActivityChamber command as follows:

S.S.1,

S1,

.01": ~StartActivityChamber(BOX);~ ---> S2

S2,

60.0”: ~StopActivityChamber(BOX);~ ---> S3

It is also possible to send the StartActivityChamber and StopActivityChamber commands from a DOS prompt. For example, to start or stop box #1 from a DOS prompt use the RUNDLL32 commands as follows:

RUNDLL32 mpdevents.dll,StartActivityChamberCmd 1

RUNDLL32 mpdevents.dll,StopActivityChamberCmd 1

Figure 9-1 - DOS Prompt Start Command



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CHAPTER 10 FILE NAMING AND TYPES

Fi le Types

Table 10-1 - File Types

File Type Description

AMD The Activity Monitor project file (Activity Monitor Data). This file contains all of the data for a project.

CSV A spreadsheet file (Comma Separated Value), which can be opened in any spreadsheet program (Excel, Calc, etc...) or text editor.

WMV A video file (Windows Media Video), which can be opened in Windows Media Player or other video playback programs.

Summary A legacy text file format containing a results summary of the data from a given session. See Chapter 11

Zone A legacy text file format containing the results of a zone analysis on a given session. See Chapter 11

Export A text file containing the raw axes data from a given session. See Chapter 11.

Fi le Naming

Summary file names are automatically generated. The file names are based upon the protocol, group, subject, and session number.

For example, if the protocol, group, subject and session number all had the value of “1”, the summary file name would be:

Protocol_1_Group_1_Subject_1_Session_1.Summary

or if the group is blank:

Protocol_1_Subject_1_Session_1.Summary



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CHAPTER 11 LEGACY DATA FILE FORMATS While the legacy data files generated by Activity Monitor 7 are similar to earlier versions, some fields have changed. Key differences to note: the date format has changed, time values are now in seconds and “Experiment Title” & “Experiment Comment” are now combined and called “Protocol Title & Comment”.

Summary Data

Summary data filenames end with the .Summary extension. Summary data files can use either the Relative or Absolute data formats. In relative reporting mode each time bin holds the sum of the data since the last time bin. When using the absolute reporting mode each time bin holds the sum of all data since the experiment began. The reporting mode will affect how the data looks when it is sent to the printer and how it looks in the summary data file. It is also used to determine how the data will be presented in the analyzed data files.

Table 11-1 - Summary Data Values

Measure (pre-analysis)

Definition (Data are presented in block intervals and session totals)

Distance Traveled The total Euclidean distance of all ambulatory episodes in centimeters or inches (see Figure 1-1). See also Defining Distance Traveled, pg. 2.

Time Ambulatory Time in ambulatory movement status. The time and distance (above) are used to determine speed.

Ambulatory Count The ambulatory rectilinear distance traveled in beams. In Figure 1-1 the ambulatory count is represented by the blue line; there are 13 ambulatory counts.

Time Stereotypic Time in seconds spent breaking beams inside the stereotypic box.

Stereotypic Counts The rectilinear distance, in beams, traveled while inside the stereotypic box.

Time Resting Time in seconds with no new beam breaks.

Vertical Counts Number of times the animal rears. Rearing is defined as concurrent beam breaks in the Z-axis and X or Y-axes.

Vertical Time Total duration in seconds of the vertical counts.

Session Time Session time in minutes.

Jump Counts Number of time periods that no X or Y-axis beam breaks were detected. This primarily occurs when the animal jumps, or on rare occasions, when the animal is rearing and the IR beams fail to contact their body.

Jump Time Total duration in seconds of the jump counts.

Average Speed Average speed in cm/s of all ambulatory episodes.

Ambulatory Episodes Recorded when the number of ambulatory counts meets or exceeds the ambulatory trigger.

Hole Board Data See Chapter 8, Inserts for Open-Field Activity.



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Analyzed Data

The analyzed data filenames end with the .zone extension. Analyzed data files can use either the relative or absolute data formats. The data analysis file contains the first 13 measures listed in Table 11-1 above plus the following values:

Table 11-2 - Analyzed Data

Measure Definition

(Data may be presented in block intervals by zone with zone and session totals)

Zone Entries The number of times the animal entered the zone from a different zone.

Zone Time Amount of time in seconds the animal is present in each zone.

NOTE: All data may be re-analyzed using different parameters, so verify the same measures are being used when performing comparative statistical analysis.

Hole Board Task Data

The hole board data filenames end with the .summary extension. If hole board strips are installed, the hole board data files may contain block information with either the relative or absolute data formats. Below are examples of hole board data files, one with hole board strips installed and one without hole board strips installed.

The hole board data file contains the first 13 measures listed in the summary data table, Table 11-1, and the following measures:

Table 11-3 - Hole Board Data

Measure Definition

Total Session Time Time necessary to run the session. This may be the task completion time or the session limit time, depending upon the setup.

Task Completion Time Time to enter all of the user-defined (task) holes.

Latency to First Hole Time elapsed between starting the experiment and entry into the first hole.

Novel Task Entries Total task holes entered at least once.

Novel NonTask Entries Total non-task holes entered at least once.

Novel Entries Entering a hole for the first time.

Repeat Task Entries Total re-entries into task holes.

Repeat Non-Task Entries Total re-entries into non-task holes.

Repeat Entries Each subsequent entry after a novel entry. These can be task or non-task



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Measure Definition

holes.

Total Entries Total number of entries for an entire session.

Average Novel Task IRT Average time between novel task hole entries.

Average Novel Non-Task IRT

Average time between novel non-task hole entries.

Average Novel Total IRT Average time between total hole entries.

Working Memory Ratio Number of novel entries into baited holes divided by the number of entries and re-entries into baited holes.

Reference Memory Ratio

Number of entries and re-entries into the baited holes divided by the total number of entries into baited and non-baited holes.

Exported Raw Data Fi les

The exported raw data files contain the raw data from the experiment in an annotated format and end with the .export extension.



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Appendix A Contact Information

Please contact Med Associates, Inc. for information regarding any of our products. Visit our website at www.med-associates.com for contact information. For technical questions, call 802-527-2343 or email [email protected].


mailto:[email protected]

Documents

Med Associates Product Manual · Med Associates, Inc. CHAPTER 2 GETTING STARTED Software Installation If the computer was purchased as part of Activity Monitor system froanm Med Associates,