NeuroWare® User`s Manual
Contents
1. ptilVlap Video Tracking Software User s Manual Version 1 0 Triangle BioSystems International 2224 Page Rd Suite 108 Durham NC 27703 Phone 919 361 2663 e Fax 919 544 3061 www trianglebiosystems com OptiMap User s Manual TBSI Table of Contents DOCUMENT OVES W nenesie ic ice 2 Shipped items list ernennen id cua geverevedcnctevaactettts 2 Software Hardware Installation 20 222044404n40nnnnnnnnnonnnonnonnnonnnnnnnnnnnnnnnnnnnnnnnnnnennnennnennnnnnnnen 2 System Requirements une caches dci dad odiada danita 2 OptiMap Installation 0 00 ccecscecsenneceesseeceeseeaeceeseeaeesseeeaecesseaaeessseaaeesseeaaeeeeseaeeeseeaaes 2 Saving amp Loading Files aid 3 Saving Files cinc iia add ibas 3 Loading FeS aeania a aia RE NETTER tia 3 intensity Detection uhren Se ee Dr br ae a Rae a iaaea eah aaa EEE EREE 4 VIGO SCtUINGS E E E E E anne sense lehn 4 Framerate nera A E E a E a E E E A E T 4 RESOIUTION WPORR PIERRE REINE NER DE EEE E EREE AEAEE EERE AEE E aE eee TE AERA EE AREAREN EEEE 4 Video Calibration mico an ebene nenne 4 Live Mode cocoa 222 een 4 A IT CHPEEITTERTERFELCHEELTETSTEREITLLHETEIETERSEERTTLTERELETETSTETLIRLEITTER 5 Threshold u a a 5 Auto Find LEDS 5 4 222 22 422er Ele 5 Conver LOMB EE ces nennen bene ek en AA AOA 6 Offline Mode au nee een dia ie ee 6 Video Recording iii ua 7 Data Editing see ee ee Een era2. amp Future Data Persistence The past and future persistence can be set individually Past data points are denoted with d and the future data points are denoted with B The current frame s data points are surrounded by a large colored circle Data in the past or future that is marked as lost by the program is denoted with x while edited data is denoted with m Data Adjustment A single data point in a single frame can be moved easily to a new location Just click and hold the data point within the circle drag the point to its new location then release This function can be performed multiple times for every data point in every frame Only the most recent positions will be saved in the new data file Data Interpolation Function To allow the program to adjust particular data points automatically navigate to a frame interval containing missing data and click the Interpolate Data button The program will perform a three dimensional x y time smoothing interpolation to adjust the positions of missing data with the selected interval Switch LEDs Sometimes LED colors are misinterpreted by the program which results in the identities of a pair of LEDs becoming switched Instead of dragging each LED marker to its correct position click the Switch LEDs button to quickly exchange the locations This button is only active when two LEDs are selected in the list box Offline Data Tracking The program will disable
3. e Recorded Video and Data File gt Load gt Data Intensity Detection OptiMap scans incoming video data and detects sources of intense light regardless of the source s color The program then identifies the color of the light source and stores its color value and location in pixels into a list visible on the control panel This detection method is ideal for experiments that involve dynamic environmental lighting Video Settings The recommended video camera can collect up to 30 frames second at a resolution of 640x480p These are the default settings upon launching OptiMap These settings may be changed to reduce the amount of data to be saved Framerate To set the video camera s framerate Video gt Framerate Resolution To set the video camera s resolution Video gt Resolution Note Changing the video resolution will reset any workspace variables defined during calibration Be sure to decide on a resolution before defining your workspace Video Calibration Live Mode In a live video recording you should first click on the CALIBRATE tab Click the Auto Calibrate button to have the program adjust the camera s light exposure and the light intensity threshold to their optimal levels this will identify any LEDs within the frame The camera will take between 10 20 seconds to calibrate Do not adjust any of the controls or light sources during this time Once the calibration has finished you can manually adjust
4. the Exposure and Threshold sliders to fine tune the video settings to your requirements Version 1 2 4 8 2013 OptiMap User s Manual TBSI Exposure Move the Exposure slider to the right to decrease the exposure and to the left to increase If the exposure is too high light reflections will be misinterpreted as LEDs Threshold Move the Threshold slider to the right to reduce the LED sensitivity If the Threshold is too low light reflections will be misinterpreted as LEDs Adjust both sliders to find the appropriate balance of visible video without false LED sensing Auto Find LEDs In addition to the Auto Calibration process LEDs can be identified automatically by clicking the Auto Find LEDs button this will not adjust the camera settings or manually by clicking the Manual Selection button After the light sources have been identified they will appear in a list see picture below The coordinates are in parentheses to denote the current locations in the video or to alert you of lost tracking Selected items in the list will be visible on screen and they can be deleted by pressing the delete or backspace keys Note Optimap s LED detection works by finding areas on the screen that are more intense than the defined threshold Therefore the threshold should be set so that the LEDs are the only objects that exceed its intensity setting Cross sectional intensity x and y can be visualized by dragging the th
5. the Record tab if you load OptiMap without connecting your camera to your PC or if you manually switch the program to its Offline Video mode Once you load a video that was not recorded with the OptiMap software the Calibrate tab will then be enabled and converted to its offline calibration mode it will have the same functionality as it does during a live video feed except that the Camera Exposure slider will be disabled and the frame slider from the Editor tab will appear beneath the video In the Calibrate tab you should choose a frame using the frame slider preferably one showing distinct light sources in the most common lighting conditions for that file You can then use the calibration buttons to locate the light sources either automatically or manually Adjust the Version 1 2 9 8 2013 OptiMap User s Manual TBSI threshold slider to optimize the light detection You can also define the workspace and length conversion at this time any frame in your video file can be used to do this Once you have finished calibrating the video it s time to return to the Record tab The Track button will automatically scan the entire video file for the light sources that you found in the Calibration tab If you are not satisfied with the tracking results ie not enough video frames were properly tracked return to the Calibrate tab and readjust your detection settings then click Track again After successful tracking you can pr
6. installation instructions 2 Navigate to the OptiMap folder within the installation disc and double click MCRinstaller exe then follow the prompts to install the MCR Library You could be required to restart your computer after installation is complete 3 Copy the OptiMap exe file and the graphics folder to the same directory in your computer You can now run OptiMap by double clicking the executable file Make sure your webcam is installed and plugged in before launching the program 4 The OptiMap tab can be found at the top right of the NeuroWare program Click this tab and then click the Start OptiMap button if you would like to run OptiMap from NeuroWare to synchronize neural data with video tracking data Saving amp Loading Files Saving Files Before initiating any recording you should choose a file directory to which you will save your data File gt Recording Directory There are two different types of files that can be saved by OptiMap e Calibration Settings File gt Save gt Calibration e Recorded Video and Data File gt Save gt Data Loading Files You can load calibration settings and video files for offline tracking Videos that were not recorded using OptiMap are acceptable for use within the software but they may yield less ideal results than those that were e Calibration Settings File gt Load gt Calibration Version 1 2 3 8 2013 OptiMap User s Manual F TBSI
7. ios 8 Interval Selecti n er s nean ae ee tddi dnd dat 8 Past amp Future Data Persistence irises cananea 9 Data Adjustment wicccssesccccesssccecevsaccedevasccecevesscedeeanccecuvenscdchsancccdusonsiedevansce re res d dias 9 Data Interpolation Function u eresseesessnsnenensnnnennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnsnnnnnnnnnsnnnnsnsnnnnnnnsnnnnnsnsnnnnnnnnnn 9 WIEN DEDOS orar dpto 9 offline Data Tracking sirier RE ea 9 Documenthistory aan a A teva sats in 10 Version 1 2 1 8 2013 OptiMap User s Manual TBSI Document Overview This document will demonstrate how to use the TBSI OptiMap video tracking software The program has the capability to detect and follow intense light sources in changing light conditions and to distinguish the colors of these light sources both online and offline calculate head orientation velocity and distance traveled and detect and interpolate lost data based on local movement patterns The system requires the use of a Windows compatible video camera TBSI recommends the Logitech HD Webcam C270 for this purpose Once the camera s drivers have been installed on the computer OptiMap either as part of NeuroWare or a stand alone application will automatically detect the device and assume control over its functionality Shipped items list e Logitech C270 camera e Optimap Installation CD if stand alone license e Collapsible camera monopod e Camera clamp S
8. oceed with adjusting your data as needed Document history V1 1 initial release V1 2 Update camera compatibility and exposure controls 8 2013 Version 1 2 10 8 2013
9. oftware amp Hardware Installation System Requirements The recommended minimum PC requirements are as follows At least 3 0 GHz Dual Core Processor 4 GB RAM 100 MB of free hard drive space 1 USB 2 0 port Windows XP OS 64 bit Service Pack 2 or later Windows 7 Logitech HD Webcam C270 included with OptiMap purchase Future support of Logitech C920 HD scheduled Q1 2014 OptiMap Installation OptiMap is available as a module within the TBSI NeuroWare software or as a stand alone application If you have purchased NeuroWare without also purchasing the OptiMap video tracking license you will be able to view and record videos within the module but you will not Version 1 2 2 8 2013 TBSI OptiMap User s Manual be allowed to save any data Please refer to the NeuroWare manual provided on our website for more details concerning installing and running the NeuroWare program The Logitech HD Webcam C270 is a plug and play USB 2 0 device Your computer will prompt you for driver installation when you plug in the camera for the first time After these drivers have finished installing you will be able to launch OptiMap after which the program will automatically detect and control the hardware To install and run OptiMap 1 Insert the OptiMap installation disc into your computer If you are installing the NeuroWare OptiMap software combo please refer to the NeuroWare manual for complete
10. reshold slider If the background environment is too bright to distinguish LEDs by intensity lowering the exposure of the camera can help Lowering the exposure also improves OptiMap s ability to identify colors If an LED is badly saturating the color it emits will appear white to the camera and therefore indistinguishable from other saturating LEDs Version 1 2 5 8 2013 OptiMap User s Manual F TBSI Auto Calibrate EXPOSURE 4 Uae sa TESOL 200 Ki IDENTIFY we Convert Length The Convert Length button is important for converting the video s pixels into two dimensions of distance x y You will need to place a ruler or some object of known length in the camera s frame for reference Follow the instructions that appear above the video to calibrate the proportions of your workspace A window will appear asking you to specify a length in cm After this step has been completed all pixel units listed in the LEDs box will be converted to centimeter units To outline your experiment s boundaries or define subspaces within the frame select the type of space you wish to create from the drop down menu in the Workspace section Next click the New Subspace button Draw the new subspace on the video frame resize if needed and click Finished when complete Offline Mode You can also calibrate a video that has already been recorded All controls function similarly to the Live Mode except that the expos
11. rsion 1 2 7 8 2013 OptiMap User s Manual TBSI Data Editing Once your recording is complete click on the EDITOR tab to assess the collected data and adjust any points that may have been lost or obscured Important To toggle the visibility of each light source s data in the viewing screen simply select it in the listbox You can Ctrl click multiple items in the listbox to show those data sets simultaneously Press the delete or backspace keys to delete selected items Interval Selection This function is useful for adjusting multiple data points simultaneously ex animal obscures light source s while remaining still qe I 1 3 OptiMap boxe Pie Video Calibration Made ADIVST DATA PERSISTENCE Track 15 HUME 20 For videos and data collected with the OptiMap software Use the lt lt and gt gt buttons to scan through and select frames in which one or more LEDs were not detected The program will cycle through missing data points for only the light sources selected in the listbox OR Use the Set First and Set Last buttons along with the slider below the video to manually select time intervals for data adjustment Use the slider to scan the video then click the Version 1 2 8 8 2013 OptiMap User s Manual TBSI appropriate Set Time button to define the beginning and end of your time interval You can also type in the times manually Past
12. ure control is disabled To switch between calibration modes use the Calibration Mode menu at the top of the screen Calibration variables can be saved and loaded within mode or across modes Version 1 2 6 8 2013 OptiMap User s Manual F TBSI Video Recording Once you have completed calibrating your video and workspace click on the RECORD tab If you haven t done so yet you should take a moment to confirm your save directory Click the a button to launch a folder browsing window Once you have chosen a save location you can click the START button to start recording your video and data If OptiMap was launched from NeuroWare clicking START will not immediately start a recording but queue the program to start when NeuroWare begins recording During the recording process you can change your Persistence and Data Density Persistence This number changes how many seconds each data point will persist in the viewing window before disappearing Data Density This number changes the number of data points shown per second BD opuvas Ea PERSISTENCE 1 thneta DATA DENSITY 30 Samprase Toggle video Toggle Data Toggle Paths Other viewing options include toggling the video feed data points and data paths The head velocity head orientation and total distance traveled are obtained using averages of position values recorded from the light source s on the animal s head Ve
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