Opto-Varimex 4 - Columbus Instruments International · 5 1.0 Specifications 1.01 Opto-Varimex 4 Basic Specifications Up to four sensor pairs (X, Y, Z, V axes) per unit Number of light

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Serial Number: ____________

(Please refer to this number for service)

Opto-Varimex 4 Activity Meter

Instruction Manual

0271-001MCopyright Columbus Instruments 2008

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Opto-Varimex 4 Operating Manual

-- Contents --

1.0 Specifications

1.01 Opto-Varimex 4 Basic Specifications

1.02 Power Requirements

1.03 Size and Weight

1.1 Introduction

1.2 Inputs

1.3 Outputs

1.4 Front Panel

1.5 Rear Panel

1.6 Sensors

1.65 Rat Sensors

1.7 Basic System Connections

2.0 Introduction

2.1 Hardware Installation

2.2 Software Installation

3.0 Running the AutoTrack Software

3.1 System Setup Configuration

3.11 Communication Port Setup

3.12 Opto-Varimex Unit Setup and Scan

3.13 Cage Configuration Setups

3.14 Saving System Setup Configurations

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3.2 Setting Up an Experiment

3.3 Experiment Running Screen

3.31 Experiment Running Live Data Display

3.4 System Tools

3.41 Cage Monitor Display

3.42 Multiple Monitor Display

3.43 Unit Monitor Display

3.5 AutoTrack Data File Viewer

3.51 Raw Data File Monitor

3.52 Raw Data File Monitor Diagnostics

4.0 Data Output Formats

4.10 File Formats

4.20 Output File Format Description

4.30 Sample Printout Format

4.40 Time In Square Printout Format

5.0 Sensor Mounting Illustrations

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1.0 Specifications1.01 Opto-Varimex 4 Basic Specifications

Up to four sensor pairs (X, Y, Z, V axes) per unit

Number of light beams: 4 to 16, depending on sensor size and type

Beam Spacing: Rat sensors -- 1 inch (2.54 cm)Mouse sensors -- ½ inch (1.27 cm)

Beam Diameter: 0.125 inches (.32 cm)

Beam Wavelength: 875 nanometers

Beam Scan Rate: 160 hertz

Maximum distance between sensors: about 20 inches (~50 cm)(depending on cage wall transparency and sensor type)

1.02 Power RequirementsMaximum of 50 watts (110 VAC, 60 HZ, or 220 VAC, 50 HZ)Fuse: 1 ampere, medium or slow acting

1.03 Size and WeightControl unit size: 14" x 11.5" x 4" (35cm x 29cm x 10cm)Control unit weight: 6.2 pounds (2.8 kg)

Sensor size and weight (per sensor pair):

4 Inch : 5" x 1.125" x 1.25" (12.7cm x 2.9cm x 3.2cm)0.2 lbs (0.1 kg)

8 Inch : 9.5" x 1.125" x 1.25" (24cm x 2.9cm x 3.2cm) 0.8 lbs (0.4 kg)

12 Inch : 13" x 1.125" x 1.25" (33cm x 2.9cm x 3.2cm)1.1 lbs (0.5 kg)

16 Inch : 17.5" x 1.125" x 1.25" (44.5cm x 2.9cm x 3.2cm)1.3 lbs (0.6 kg)

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1.2 Inputs

Each Opto-Varimex 4 unit can control up to four sensor pairs.

The sensor input signals to the Opto-Varimex 4 connect through four black RJ-45 typeconnectors located next to each other on the rear panel. These are labeled X,Y, Z, and V.

Each Opto-Varimex 4 sensor pair consists of an Emitter, with four to sixteen infrared diodeoptical beam emitters, and a Detector, with four to sixteen phototransistor beam detectors.

The Emitter plugs into either of the two RJ-45 jacks on the Detector. The remaining Detectorjack plugs into the X, Y, Z, or V inputs of the Opto-Varimex 4.

Opto-M3 commands and data are sent and received from the controlling computer systemthrough the two beige CI-BUS jacks wired in parallel. The CI-BUS is a multiple-drop RS-422system, and the Opto-Varimex 4 units have two CI-BUS jacks so they can be easily daisy-chained together to form a larger system of multiple units.

* * * Important Note * * *

Do NOT plug the sensor pairs into the CI-BUS jacks!

Do NOT plug the computer connection cable into the X, Y, Z, or V inputs!

1.3 OutputsOpto-Varimex 4 data is only available through the beige CI-Bus serial interface output jackswhich are connected through an adaptor box to the control computer.

The RS-422 connection on the Opto-M3 must be converted to a standard RS-232 serial portsignal to interface to most computers. Large Oxymax systems will have a special multi-rateinterface box for this purpose. Single Opto-Varimex 4 systems will have a small converter box.A CI Bus to USB converter box is also available.

The CI-BUS jacks are used to connect additional devices on the CI Bus. If the Opto-Varimex 4 isthe last device on the bus, install a CI-BUS terminator in the empty CI-BUS jack.

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1.4 Opto-Varimex 4 Front Panel Controls

1. Power On Indicator: this LED should be illuminated when the unit is turned on.

2. Power Switch: applies main AC power to the Opto-Varimex-4

3. Data In LED: will light up whenever the computer controller scans the Opto-Varimex-4 system for new data.

4. Data Out LED: will light up when this particular unit responds with new data.

5. Reset Button: will manually reset the internal beam-break counters. This shouldNOT be pressed during a long-term, computer-controlled experiment!

6. LCD Sensor Count Display: this LCD display shows the current raw and“ambulatory” counts for each of the four sensors plugged into the Opto-Varimex 4.

The first count is “raw”: every interruption of one of the optical beams is registered asa count. The second “AMB” (AMBULATORY) count is processed: it only registersa count if a NEW beam is interrupted. The AMB count will not respond to repeatedbreaks of a single optical beam, which can often happen with stereotypic digging orgrooming activity.

Note: if there is no sensor plugged into the Opto-Varimex sensor input, or if a sensorthat is plugged in is showing that ALL beams are broken, a “------“ series of dasheswill show instead of a beam count.

The LCD contrast is controlled by an internal adjustment potentiometer. It is set at the factoryfor optimum contrast, but this may need to be adjusted if the unit is operated in an environmentwith markedly higher or lower ambient temperatures.

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1.5 Opto-Varimex 4 Rear Panel Connections

1. The CI-Bus Connections: these RJ-45 connectors are used to connect the Opto-Varimex 4unit to an external computer controller. Two connections, wired in parallel, are provided so thatmultiple Opto-Varimex 4 units can be connected in a “daisy-chain” manner with each having acable extending to the next unit.

2. Sensor Input Connections: each Opto-Varimex 4 unit can have up to four external opticalsensor arrays. These can be used in several ways:

Each X, Y, Z, and V, sensor can be used as a basic single-axis activity monitor for a single cage.

Normally, the X and Y sensor inputs are used to track the full horizontal activity in a single cage.

The “Z” and “V” sensors can be used in addition to detect vertical activity in a single cage, orcan be used as the horizontal “X” and “Y” axes of a second cage.

3. The fuses for the Opto-Varimex 4 are either USA or European standard. They should bereplaced with a 1 ampere fuse with a slow time constant.

4. The AC power inlet of the Opto-Varimex 4 is a standard IEC-320 connector. The properpower cord will be sent with the unit whenever possible. By using the standard IEC-320connector any specific power cord should be locally available. The universal power supply inthe Opto-Varimex 4 will operate on any AC mains voltage from 50-60 Hz, 100 to 240 VAC.

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1.6 SensorsThe Opto-Varimex 4 system can be configured for any combination of up to four sensor pairs.Usually one to three sensor pairs are used for each subject cage, monitoring activity in the X, Y,and Z (vertical rearing) axes. Sensors have either ½” (Mouse) or 1” (Rat) beam spacing.

Fig. 3 -- 4 inch and 8 inch Mouse SensorsA sensor pair consists of an Emitter, which sends out pulsed infrared beams, and a Detector,which picks up these optical pulses from four to twenty inches away, depending on the sensortype. The Emitter has a single RJ-45 connector and a clear window behind the beam holes. TheDetector has dual RJ-45 connectors and a dark IR filter window behind the beam holes.

The Emitter connects to the Detector with a short jumper cable. The Detector then connects witha longer cable to one of the four inputs on the Opto-Varimex 4. Either RJ-45 jack on theDetector can be used for the Emitter and Hub Box connections.

The beam holes on the sensors are deliberately offset to one end. This allows stacking thesensors end-to-end for special setups and lets them fit better on the Columbus Instrumentsspecial CLAM system cages that have external ports and fittings.

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1.65 Rat SensorsThe rat sensors for the Opto-Varimex 4 are available in three basic sizes, 8 inch, 12 inch, and 16inch. The longest, R16, sensors will normally operate up to twenty inches apart through a clearcage. Note that when using discolored, worn, dirty, or molded Nalgene cages, the range may besignificantly reduced.

Fig. 4 -- 8 inch, 12 inch, and 16 inch Rat Emitters

The rat sensors connect just like the mouse sensors, but have the optical beams on one inchcenters. This makes results from the rat sensor systems directly comparable to the olderColumbus Instruments Opto-Varimex, Opto-Minor, Opto-Mini, and Opto-Max systems. Rat andMouse sized sensors can be mixed in a single Opto-Varimex 4 system.

1.7 Basic System ConnectionsThe second RJ-45 connector on the Detector sensor plugs into one of the four axis inputs. TheCI-Bus output of the Opto-Varimex 4 is plugged into a CI-Bus Adaptor Box, which then plugsinto the computer controller’s serial or USB port, depending on the Adaptor Box model.

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2.0 IntroductionThe Columbus Instruments Opto-Varimex 4 is the latest in a long line of optical beam activitymonitors. Designed to replace the original Opto-Varimex activity monitor frame, it consists of acompact control unit that supports a wide variety of optical beam sensor types andconfigurations. Up to four sensor pairs connect to a single Opto-Varimex 4 control unit. Alarge backlit LCD display on the front panel displays the TOTAL and AMBULATORY beambreak counts for each of the four sensor pairs in real time.

Every time a beam is broken, a TOTAL count is accumulated. An AMBULATORY count isaccumulated every time a NEW beam is broken. The AMBULATORY count does not respond tothe same beam being broken and restored repeatedly. This keeps the AMBULATORY countsfrom responding to rapid beam interruptions caused by scratching, grooming, digging, or otherstereotypic non-ambulatory movements. By recording the counts accumulated by the TOTALand AMBULATORY counters it is possible to compare amounts of ambulatory and stereotypicmovements.

The Sensor Pairs consist of an infrared Emitter bar, with four to sixteen infrared beams, and amatching Detector bar. Sensor cabling uses convenient snap-fit RJ-45 connectors and sensorpower is supplied from the Opto-M3 controller over the signal cables so no external sensorpower supplies are required.

2.1 Hardware InstallationEnsure that the Opto-Varimex 4 control unit is powered OFF before making any connections.Mount the sensors on the supplied brackets with emitters facing detectors. Because the sensorbeams are scanned sequentially, the sensor pair MUST have their connector ends on the sameside of the cage. To avoid interference, Vertical sensors should be mounted upside-down so thatboth Emitters are not on the same side.

The sensors each have four pairs of threaded mounting holes on ¾” centers: a pair on each endand two pairs on the back. The holes used for mounting the sensors depend on the cage andbracket configuration. Multi-level brackets with multiple mounting holes usually have the holeson ½” centers. When using these brackets a single bolt is used to mount each end of the sensor.By using the upper or lower sensor hole, the sensor height can be adjusted in ¼” increments. Ifusing a single bolt mounting, the bolts must be tight so that the sensors will not rotate out ofalignment.

* * * IMPORTANT NOTE * * *

Do not screw any mounting bolts more than 3/16” into the sensors!

The standard mounting hardware is a 6-32 x ¼” pan head screw. If longer hardware isrequired for custom brackets use spacers or washers to be sure that the mounting bolts arelimited to a 3/16” projection into the sensor shell.

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With the short flat jumper cables, connect each single Emitter jack to one of the double Detectorjacks. Note: usually an Emitter and Detector sensor pair are connected together, but an Emittercan connect to ANY Detector jack without affecting system operation.

Now, use the long (two meter) flat cables to connect each of the remaining Detector jacks to acorresponding Opto-Varimex 4 sensor connection jack. This is where you must decide whichsensor is to be the X, Y, Z, or V axis.

If you are using the AutoTrack software you must now connect another long flat cable from onethe Opto-Varimex 4 CI-Bus connection jacks to the CI-Bus Adaptor Box which, depending onthe model, will then plug into the computer controller with a serial or USB type cable.

If your system has more than one Opto-Varimex 4 unit, use the long flat cables to connect theother CI-Bus jack to the next unit, and continue the “daisy-chain” cabling to the last unit. Thelast device on a long CI Bus run, should have a small, orange, CI Bus terminator plugged into theunused CI-Bus jack. A single Opto-Varimex does not usually require the CI Bus terminator.

Now, turn on the Opto-Varimex 4 control unit. The front panel LCD should light up. Each X,Y, Z, and V sensor input has a single line on the display. If no sensor is plugged in, or if thesensor has all beams blocked, a line of dashes (- - - - -) will appear for that sensor. If the sensoris responding, the count should be “00000” for the regular and AMB (ambulatory) count.

Move your finger, or a pencil, down along the sensor bar, obstructing each optical beam in turn.You should see a count on the LCD display that matches the number of beams in the sensor. Ifnot, try readjusting the sensor angle to aim directly at the opposite side. If using a cage, tryremoving it temporarily to see if this brings a weak beam back. You should always get the fullbeam count on the LCD display with an empty cage, unless one or more of the beams areobstructed by cage walls, molded corners, water bottles, etc.

2.2 Software Installation The Opto-Varimex 4 can be controlled by the Columbus Instruments Opto-Varimex 4AutoTrack System program. First, disconnect the CI-Bus Adaptor box cable from the computer.To install the software insert the CD in your computer’s CD drive. Open the Windows ControlPanel, and select the Add/Remove programs utility. Click on the Add New Programs icon, andfollow the prompts to start the installation program.

Important Note:

During the installation, if you are warned that certain files on the installation CD are olderthan your currently installed files, ALWAYS select the button to keep the newer files!

You can now plug in the CI-Bus Adaptor box. If you are using the CI-Bus to USB Adaptor box,the Windows system will detect it, and request Driver installation software for it. Follow theprompts for “have disk”, and choose the drive still holding the AutoTrack installation CD.Windows should be able to locate the drivers on the CD and will install them. In a moment,Windows will request drivers again. This is for the “virtual serial port” used by the CI-Bus USBAdaptor. Follow the same process above, and a new Windows COM port will be installed.

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3.0 Running the AutoTrack SoftwareThe top menu bar of the Opto-Varimex 4 AutoTrack System is used to set up Opto-Varimex 4system configurations, experiment parameters, and to open and view previously acquired data.

The top menu options are as follows:

File: Allows you to Open existing data files, or Exit the program.

Edit: Will allow you to Copy and Paste text data in appropriate screens.

Experiment: To Setup and Run a new experiment.

Tools: An important menu item.

The first selection is the Cage Monitor: it will display the X-Y path of a subject for a singlecage, and show detailed current counts and data information for that cage.

The second selection is Multiple Cage Monitor: it will display the X-Y path and basichorizontal beam count for up to eight cages at the same time.

The third selection is System Setup: this special screen allows you to completely specify yourcurrent AutoTrack system so the AutoTrack software can properly tabulate the data. Unlike theolder Opto-Varimex AutoTrack systems, where each Opto-Varimex monitored a single subjectcage, the Opto-Varimex 4 system allows a single unit to monitor two cages with full X-Ytracking, or up to four cages with simple single-axis activity monitoring like the ColumbusInstruments basic Opto-Mini system. Combined with the options of five different sensor types,and the ability of a single Opto-Varimex to monitor multiple cages, the possibilities are many.

The System Setup screen gives a complete look at the system configuration, allows easy testscanning for Opto-Varimex units, provides selection of any existing serial port, and allows youto save unique setups in your own file system, as well as the default Opto4.ini file which is usedwhen the program starts up.

Last is the Opto 4 Unit Monitor tool. This is a basic sensor monitor that focuses on the Opto-Varimex 4 unit itself, rather than the cage configuration. It can be used to quickly verify properoperation of any given Opto-Varimex 4 unit in the connected system.

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3.1 System Setup ConfigurationClick on the top menu Tools item, then select System Setup to open the following screen:

The System Setup screen is divided into three major sections. The column on the left deals withthe Opto-Varimex 4 units themselves. The large table in the center deals with the individualsubject cages. The bottom section is used to select the COM port, and save the configuration.

3.11 Communication Port Setup

The proper COM serial port must be selected before the AutoTrack software can scan any activeOpto-Varimex 4 units. At the bottom of the System Setup screen is a Select Serial Port combobox that will show the available ports on the computer. Select the port, then click the Scanbutton to the left to see if the active Opto-Varimex 4 units respond.

3.12 Opto-Varimex Unit Setup and Scan

Click on the Scan button on the bottom left to see what units are currently turned on andconnected to the system. Units are shown by their actual CI-Bus address (239-246 for the Opto-Varimex 4 product), and the address box will turn from inactive background gray to white if theunit is active. If an active unit address box is clicked, it will change from white to a green color.

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On the top of the screen is the Unit Sensor Type frame. The address of the currently selectedunit will appear as a light green label. You can now use the X, Y, Z, and V combo boxes to tellthe system what sensors are connected to that unit. You can choose any of the five sensor types,or “none.” Each of the active Opto-Varimex 4 units should have their connected sensor typesentered in this way.

3.13 Cage Configuration Setups

The large table in the center deals with the individual subject cages. Each cage has a line in thetable. Each cage can have up to four unit sensors mounted on it. The X and Y sensors measurehorizontal activity. The additional Z and V axis sensors usually measure vertical activity(rearing, leaps, or hole-pokes.) If you click on any cage line, the top frame caption will changeto Cage Sensor Configuration, and the label will change color to a light blue with the cagenumber indicated. As with the units, the X, Y, Z, and V combo boxes are used to indicateexactly which unit (239-246) sensor (X-V) is being used for this cage axis.

Important note:

In order to provide more flexibility, it is possible to “force” the Setup System to set up units andcages that are not physically present. This allows setting up future system configurationswithout requiring the actual hardware to be connected and active. Double-clicking on a Unitaddress button will temporarily enable that unit so you can define the sensor types for it.Double-clicking on a cage line can be used to enable, or disable a cage in the setup. A disabledUnit or cage will appear in the background gray color, instead of the normal active white.

Be careful when entering the cage configurations; it is easy to accidentally “double-click” anddisable a cage and the light-blue selected cage “highlight” can hide this condition. When youhave finished configuring all the cages, be sure to click in one of the blank cage rows near thebottom to be sure that all configured cages are active, and not “grayed-out.”

3.14 Saving System Setup Configurations

When the Units, Cages, and COM port have been set up properly, save the system configurationto a file. Click on the Save Config button to open a file requester, where you can save the setupunder a unique name, or as the default Opto4.ini file. Note that Setup Configuration files arealways saved with the “.ini” file extension.

It is a good idea to save your common setups as files, which can then be easily loaded byclicking the Load Config button. Loaded setup configurations can be easily edited as needed.

When you click the Back button or X to leave the Setup screen, you will be asked if you wish touse the new setup, and then if you wish to save it. You do not need to save the setup again if ithas been saved previously or is the default setup. If you have just saved the setup, it will be usedas the current configuration when you exit the Setup screen.

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3.2 Setting Up an Experiment

To set up and run an experiment, select the top menu Experiment, then Setup. The screenabove will appear. The number of cages and configuration of Opto-Varimex 4 sensors must bealready configured in the Setup System section of the program.

In this screen, you must first select an output data file for the experiment (a tabulated, .CSVspreadsheet compatible file) by clicking on the file name text, or the Browse button. Enter thetotal experiment length in minutes, and the Ambulatory Box Size. The Ambulatory Box Sizeshould normally be set to 1 beam, but can be as high as 4 beams for large, rapidly movingsubjects.

If you want to save the actual tracking data for the subject, to see the pattern of movement afterthe experiment is finished, you must select the Save Raw Data checkbox. The raw data file willhave the same name as the experiment file, but with a “.R” file extension.

If the Delayed Start checkbox is set, the current system time, and a box to enter a future starttime will appear. If a Delayed Start is set up the experiment can still be manually started early.

A textbox area is provided for entering general notes about the entire experiment. In addition, aCage Comments box is provided with individual comment lines for each subject cage.

When you are ready to go to the Experiment Running screen, click the Start button – note: thiswill display the next screen, but will NOT immediately start the experiment.

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3.3 Experiment Running Screen

The above screen shows an experiment all set up and waiting for an automatic delayed start of allcages in about seven minutes. The AutoTrack system allows complete “staggered start” controlwhen needed for an experimental study. Click on a cage line number to select it, then click theindividual cage Start button to start (or Stop) that cage at any time. The experiment will notfinish until the last cage is done.

Although data for each cage is acquired on a second-by-second basis, the data is only saved tothe total data file once per minute. Be aware that if you click the Back button, and then chooseto end the experiment prematurely, you may lose up to one minute of previous data.

Along with individual staggered starts, cages may be individually halted if necessary. Thedefault one-minute session interval is flagged as being incomplete, but the data up to the halt issaved on the next cycle. When the cage is started again, data acquisition begins right away, anda new staggered cycle of interval start and stop times begins.

This halting of a single cage during an experiment is to provide adaptability to unforeseenproblems during a large experimental run. It should not be used as a standard operatingprocedure.

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3.31 Experiment Running, Live Data Display

The normal Experiment Running screen will show live data updates of some basic parameters foreach of the subject cages, along with the time remaining for each individual cage.

In addition, it is possible to open the Cage Monitor or even the Multiple Cage Monitor screenswhile an experiment is running to observe live tracking data from the experimental subjects.

Screens opened during an experiment will automatically shut down when the ExperimentFinished message box is acknowledged.

While there should be no problem viewing these screens in real-time, it is always prudent toavoid excessive screen flipping and mouse movement during an experiment. Although the Opto-Varimex 4 system has extensive data buffering, the Microsoft Windows operating system doesnot always respond promptly to serial port data access requests from external hardware. For thebest results, do not run any other programs concurrently during an experiment.

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3.4 System ToolsThe System tools, Cage Monitor, Multiple Cage Monitor, System Setup, and the Opto4 UnitMonitor are available by clicking the top menu Tools item.

3.41 Cage Monitor Display

The basic Cage Monitor tool of the AutoTrack system can quickly show you how well a givencage setup is currently operating. Using the current system configuration set up in the SetupSystem screen, each cage can be selected individually. Along with showing basic X-Y tracking,the Monitor will show current counts and calculated data in real time. By clicking on the ShowBeams checkbox, the X and Y horizontal beams will show as red lines when they are interrupted.This is a good way to check all the horizontal beams for a given cage in a single screen. If Z andV vertical axis sensors are also associated with the cage, the Z and V beams will show up as bluelines when they are interrupted. The Freeze checkbox allows you to immediately halt dataacquisition in the Monitor mode. Data flow will resume when the Freeze box is un-checked.

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3.42 Multiple Cage Monitor Display

The Multiple Cage Monitor can show the basic X-Y activity in up to eight cages at once. Thetotal horizontal axis (X+Y) counts are also displayed for each cage. This screen provides a quickview of the system operation. It also has the Show Beams and Freeze display features of thesingle cage monitor.

The Multiple Cage Monitor can be used while an experiment is running to monitor the actualactivity of multiple subjects. This can be a good way to watch for particular problems in dataacquisition during the experiment itself.

Note that up to eight cages can be monitored at once, as above, but the system will only showcages that have been set up in the current operating configuration. In the above system, theOpto-Varimex 4 units for cages five through eight were deliberately disabled -- resulting in theimmediate display of no tracking, and all beams broken for these cages.

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3.43 Opto-Varimex 4 Unit Monitor Display

The Opto4 Unit Monitor display provides a quick way to check out the individual unitsconnected in an AutoTrack system without worrying about the current system configurationsetup.

The Opto-Varimex 4 Units are selected by their address number, which is usually the last threedigits of the serial number on the unit, for easy identification.

The X, Y, Z, and V total and ambulatory (AMB) counts should always match the countsdisplayed on the Opto-Varimex 4 front panel LCD display when the unit is scanned.

The X and Y axis interrupted beams are shown as red lines. The Z and V axis beams will showas blue lines when interrupted. The Z axis display is parallel to the X axis, but slightly offset toshow the two sets of beams clearly. The V axis is similarly displayed in the Y axis direction.

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3.5 AutoTrack Data File Viewer

Open the AutoTrack Data File Viewer screen by selecting File, Open from the top menu. A filerequester will appear, and will display only processed AutoTrack “.CSV” files. If a raw data filefor the same experiment is available, it will be noted at the bottom of the screen. It is importantto keep the “.R” raw files and the “.CSV” processed data files for an experiment in the samelocation because the AutoTrack Data File Viewer needs both files to display raw data.

Once a data file has been opened in the File Viewer, there are several options. On the bottomleft of the screen is an Interval Minutes entry box. The processed data is saved in one-minuteintervals by default, but the displayed data can be rapidly reformatted for longer intervals. If theexperiment length is not evenly divisible by the new interval value, the re-formatted data willindicate that the last interval is short. The reformatted file can be saved back to disk. Thestandard default name will be the original name with “_N” added, where N is the new IntervalMinute value. Note that such reformatted files can be opened later in the File Viewer, but onlyfor display – no further interval formatting or raw data linking is allowed. The displayed data canbe printed in a basic Courier font to the Windows default printer by selecting File, then Printfrom the top menu. For more customized hardcopy, the text in the File Viewer screen can beselected, and then copied with the top menu Edit, Copy selection. This text can then be pasteddirectly into any word-processing program for further formatting. The standard AutoTrack .CSVfiles can also be opened directly in a spreadsheet program such as Excel and formatted andmanipulated there as well.

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3.51 Raw Data File Monitor

Once the Data File Viewer screen has opened an AutoTrack data file that has an associated rawdata file, the Monitor and Multiple Monitor options are available under the top Tools menu.When viewing recorded data, the Monitor allows you to select the data interval to display.

If the file has been reanalyzed with a different interval, the Monitor will show the total activityformatted for the new interval length. The actual start and stop times for the displayed intervalare always shown at the bottom of the Select Data Interval frame.

The Multiple Monitor will allow a similar scrolling through the intervals, but, due to the issueswith staggered start files, it will only show the intervals, not the start and stop times, for themultiple cages.

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3.52 Raw Data File Monitor Diagnostics

In addition to the basic Data File Monitor mode, a special “diagnostic” mode is available. Onthe top menu bar, select Tools, then go down to the Diagnostic selection and click on it. SelectTools again, and you will see that the Diagnostic item is checked. Select the Monitor from theTools menu with the Diagnostic item checked and you will see a different version of the Monitordisplayed, as shown above. In addition to the Select Data Interval frame, a Diagnostic Sampleframe will appear. By clicking on the [<] and [>] buttons, or typing a number in directly, youcan select and display any of the 600 samples taken during a standard one minute interval.

Along with the activity track, the actual optical beams that were interrupted during any given 100millisecond interval are clearly shown. By clicking and holding down the mouse button on oneof the Diagnostic Sample direction buttons, the samples can be scrolled through at approximatelyreal-time speed, replaying the actual movement of the subject.

Note: you should only use the original one-minute interval file when applying the specialDiagnostic mode.

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4.0 Data Output Formats

4.10 File Formats

The Columbus Instruments Opto-Varimex 4 AutoTrack software saves processed experimentdata in a comma-separated ASCII format (.CSV) that can be directly opened by most spreadsheetand data analysis packages. The main differences are between the normal mode, where all cagesare started simultaneously, and the staggered start, where each cage in the experiment is startedindividually. When in the staggered-start mode the experiment will not end until the last cage’sfinal interval is over.

In addition to the processed data file, the AutoTrack software can save “raw” data. This optionmust be selected in the Experiment Setup screen. The raw data files are large – about 6000 bytesper minute for each Opto-Varimex 4 in the system. While not suitable for long-term (multi-day)experiments, the raw data file option is highly recommended for shorter experiments. The rawdata preserves every optical beam state for every sensor in the system ten times a second. Thisallows a detailed examination of activity and provides valuable trouble-shooting information.The raw data is also required if you wish to do a Time In Square analysis of a subject’s X-Yactivity after the experiment.

4.20 Output File Format Description

The processed data output files from the AutoTrack have the following format:

All files begin with a information header. This includes the experiment file name and full datapath, the date and time the experiment started, the length of the experiment, and a block forexperiment comments entered in the Experiment Setup screen, and a note if there is acorresponding raw data file.

The second part of the header lists the number of cages, the stereotypic box size, and another textblock for comments added for the individual cages.

The main body of the file follows with the data from each cage. Each cage interval has a singleline that lists, in this order:

1. The interval number (Int)2. The cage number (C#)3. The interval start time (Start)4. The interval stop time (Stop)5. The distance in centimeters traveled by the subject during the interval (DT cm)6. The resting time (no movement detected) in seconds (RT sec)7. The stereotypic time (small movements) in seconds (ST sec)8. The ambulatory time (large ambulatory movement) in seconds (AT sec)9. Bursts of stereotypic movement (BSM)

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10. Horizontal counts – the combined total of all X and Y axis counts (HC)11. Ambulatory counts – combined X and Y, but only for new beam breaks (AC)12. Vertical sensor counts – total counts from the Z axis sensor (V1C)13. Vertical sensor breaks – single vertical rearing events with one second between (V1B)14. Clockwise rotations (optional) (CR)15. Counter-clockwise rotations (optional) (CCR)16. Second vertical sensor (V axis) counts (V2C)17. Second vertical sensor (V axis) breaks (V2B)

These seventeen columns of data are always present, whether or not they are used by theparticular cage in the system. Unused or inactive items will simply have zeros for the data.

4.30 Sample Printout Format

A small Courier font is used to compress the data from multi-sensor systems on to a single page.For different formatting load the data files into a spreadsheet program then select, reformat, andprint the data directly from the spreadsheet.

Opto-Varimex 4 AutoTrack System DataExperiment Name: C:\Program Files\Opto4\Data\mg080408bExperiment started: 4/8/2008 2:59:58 PMExperiment Length: 4 minutes,Experiment comments: -- Raw data saved in separate .R file

Number of Cages: 4Stereotypic Box Size: 1Cage Comments:1 -2 -3 -4 -

Interval length: 1 minute

Int, C#, Start, Stop, DT cm, RTsec, STsec, ATsec, BSM, HC, AC, V1C, V1B, CR,CCR,V2C,V2B1, 1, 14:59:58, 15:00:58, 797, 9, 1, 50, 1, 201, 166, 0, 0, 0, 0, 0, 01, 2, 14:59:58, 15:00:58, 848, 9, 1, 50, 1, 229, 182, 0, 0, 0, 0, 0, 01, 3, 14:59:58, 15:00:58, 0, 60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 01, 4, 14:59:58, 15:00:58, 0, 60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0

2, 1, 15:00:58, 15:01:58, 953, 3, 2, 55, 2, 254, 213, 0, 0, 0, 0, 0, 02, 2, 15:00:58, 15:01:58, 1002, 3, 1, 56, 1, 295, 223, 0, 0, 0, 0, 0, 02, 3, 15:00:58, 15:01:58, 80, 56, 0, 4, 0, 36, 31, 16, 0, 0, 0, 0, 02, 4, 15:00:58, 15:01:58, 80, 56, 0, 4, 0, 36, 31, 16, 0, 0, 0, 0, 0

3, 1, 15:01:58, 15:02:58, 179, 50, 0, 10, 0, 53, 42, 0, 0, 0, 0, 0, 03, 2, 15:01:58, 15:02:58, 199, 50, 0, 10, 0, 57, 52, 0, 0, 0, 0, 0, 03, 3, 15:01:58, 15:02:58, 584, 25, 2, 33, 2, 303, 276, 130, 0, 0, 0, 0, 03, 4, 15:01:58, 15:02:58, 584, 25, 2, 33, 2, 303, 276, 130, 0, 0, 0, 0, 0

4, 1, 15:02:58, 15:03:58, 961, 0, 3, 57, 3, 257, 201, 0, 0, 0, 0, 0, 04, 2, 15:02:58, 15:03:58, 1060, 0, 2, 58, 2, 279, 212, 0, 0, 0, 0, 0, 04, 3, 15:02:58, 15:03:58, 0, 60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 04, 4, 15:02:58, 15:03:58, 0, 60, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0

1,, Totals: ,, 2890, 62, 1, 172, 6, 765, 622, 0, 0, 0, 0, 0 2,, Totals: ,, 3110, 60, 4, 174, 4, 863, 670, 0, 0, 0, 0, 0 3,, Totals: ,, 664, 201, 2, 37, 2, 339, 307, 146, 0, 0, 0, 0 4,, Totals: ,, 664, 201, 2, 37, 2, 339, 307, 146, 0, 0, 0, 0

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4.40 Time in Square Printout Format

Opto-Varimex 4 AutoTrack System DataExperiment Name: C:\Progarm Files\Opto4\Data\mg080408bExperiment started: 4/8/2008 2:59:58 PMExperiment Length: 4 minutes,Experiment comments: -- Raw data saved in separate .R file

Number of Cages: 4Stereotypic Box Size: 1Cage Comments:1 -2 -3 -4 -

TIME IN SQUARE ANALYSIS Interval Length: 1 minute

Int,C#, S1, S2, S3, S4, S5, S6, S7, S8, S9, S10, S11, S12, S13, S14, S15, S16

Number of Entries to Each Square1,1 ,2,5,7,4,1,2,3,5,1,1,0,2,2,3,2,11,2 ,2,5,8,6,1,2,4,5,1,1,0,2,2,3,2,21,3 ,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,01,4 ,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

Amount of Time Spent in Each Square (seconds)1,1 ,13.4,4.0,8.6,3.5,1.8,1.3,1.4,5.6,1.9,1.4,0.0,3.8,4.2,4.3,2.8,2.01,2 ,13.3,3.8,7.6,4.2,1.8,1.4,2.0,5.3,1.9,1.4,0.0,3.8,3.9,4.3,3.0,2.31,3 ,60.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.01,4 ,60.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0






Amount of Time Spent in Each Square (seconds)4,1 ,0.7,0.2,2.3,0.0,3.5,3.7,2.9,0.0,5.2,7.6,2.6,0.0,17.4,5.2,4.2,4.54,2 ,0.7,0.4,3.0,0.0,3.2,3.0,2.6,0.0,4.4,7.9,3.8,0.3,16.8,4.9,4.7,4.34,3 ,0.0,0.0,60.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0

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4,4 ,0.0,0.0,60.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0

Total Number of Entries to Each SquareCage,1,7,8,11,8,11,12,7,7,12,20,7,6,12,18,9,5Cage,2,7,8,11,9,11,12,8,7,10,22,9,5,11,17,8,5Cage,3,4,6,9,7,6,2,3,6,5,1,1,3,3,1,1,2Cage,4,4,6,9,7,6,2,3,6,5,1,1,3,3,1,1,2

Total Amount of Time Spent in Each Square (seconds)Cage,1,74.0,6.7,13.1,12.2,10.4,8.1,5.7,6.7,10.7,21.2,4.8,7.0,24.8,15.2,10.7,8.7Cage,2,74.4,6.7,12.3,13.5,9.7,7.9,6.2,6.3,9.8,19.8,6.9,5.8,23.7,15.2,11.5,10.3Cage,3,119.2,2.8,90.2,8.1,2.8,0.8,0.5,2.9,2.7,0.5,0.4,0.9,6.2,0.2,0.5,1.3Cage,4,119.2,2.8,90.2,8.1,2.8,0.8,0.5,2.9,2.7,0.5,0.4,0.9,6.2,0.2,0.5,1.3

The Time In Square analysis is a basic place-preference analysis that divides the standard Opto-Varimex arena into a four by four grid of sixteen squares. This system is provided to allowdirect comparison with TIS studies done over the last two decades with Columbus InstrumentsAutoTrack systems.

Note: the sixteen X-Y squares used in the Time In Square analysis are defined as follows:

13 14 15 16

9 10 11 12Y axis

5 6 7 8

1 2 3 4

X axis

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5.0 Sensor Mounting IllustrationsOpto-Varimex 4, 16” Sensor Cage Assembly

The Opto-Varimex 4 sensor pairs, Emitter and Detector, must be mounted directly across fromeach other. With both connector ends at the same side of the cage. A short RJ-45 connectorcable connects the Emitter into either one of the two jacks on the Detector. The Detector’sremaining jack connects to one of the X, Y, Z, or V inputs of the Opto-Varimex 4. The 16”sensors are mounted around a standard 17”x17”x8” cage by bolting the ends of the sensors tofour corner brackets. IMPORTANT: Use ¼” long 6-32 mounting screws only!

Top view of cage, brackets, and sensor assembly.

Each Emitter and Detector has two 6-32mounting holes on the ends. These holesare on ¾” centers. The holes in the standardbrackets are on ½” centers.

BOTH HOLES WILL NOT LINE UP WITHTHE BRACKET HOLES AT THE SAMETIME.

The sensors are designed to be mounted witha SINGLE ¼” screw at each end. By usingthe top OR bottom mounting hole, the sensorheight can be adjusted in ¼” increments.

This close-up view of the lower-right-handcorner bracket shows the mounting screwsand the cabling.

The lower right-hand sensor is a Detector,with two connectors. The upper sensor (forrearing detection) is an Emitter, pointing atand connected to its corresponding Detectoron the other side.

The upper sensor pair is mounted upside-down. This allows the optical beam planesto be much closer together, and will placemost of the cables at one end of the cage.

It is important not to put both Detectors onthe same cage side, as the two pairs ofsensors may then interfere with each other.

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OPTO-VARIMEX 4 SENSOR MOUNTING ON “U” BRACKETS

Rat-16 sensors mounted on standard U-brackets with thumbscrews.

The Opto-Varimex sensors have four mounting holes near each end, ¾ inch apart,on the sides, and on the back. Within the limits of screw projection into the sensorbox: no more than 3/16” (4.7mm), any of the mounting holes can be used with anybracket system to secure the sensors.

Note: regular 6-32 screws can be used for permanent mounting of sensors, butscrew length must not exceed ¼”!

Sensors are normally secured with a SINGLEscrew on each end. The screw can be in the upperor lower sensor hole, allowing adjustment ofsensor height in 0.25 inch increments with thestandard U and Corner brackets.

With 1/4” spacing of bracket holes, sensors canhave both mounting holes used for a more rigidlyaligned assembly.

The Emitter cable connects to the extra RJ-45 jackon the corresponding Detector. The Detector thenconnects to one of the Opto-Varimex 4 sensorinputs.

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Documents

Opto-Varimex 4 - Columbus Instruments International · 5 1.0 Specifications 1.01 Opto-Varimex 4 Basic Specifications Up to four sensor pairs (X, Y, Z, V axes) per unit Number of light