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1. 0 u This option divides the data in fixed time blocks by default this block size is 30samples and visualized each of the green or blue segments of the threshold line If the signal falls any time within a block below the threshold green and blue line then the activity counter is incremented by 1 Threshold is calculated on every point of time On The Fly by the algorithm 1 Threshold Average Default algorithm for liquid and solid medium In this option every time the signal falls below threshold the activity counter is incremented The threshold line is also calculated On The Fly at all times NOTE There s a third detection algorithm design for very small organisms that don t travel through the medium but this algorithms is only accessible after the run 19 is concluded Groups sub menu The Groups sub menu allows selecting the wells associated to an experimental group biological or technical replicates Conf i gi Biological Replicate Groups gt G roups S Assigned channels Free channels Output y Tools 04 Group4 005 Groupb uu CLEAR LIST Groups are identified with a 3 digit number from 000 to 383 plus the assigned name When channels are loaded into a group then a new free group will appear into the list The name of each group can be modified by double clicking in it from the list The mean of all Channel Wells associated to a group will be plotted in the main screen Ho2. Tab Pause Il Pauses the current acquisition lapse the system does not keep track of the time it remains paused Stop E Stops the current data acquisition During acquisition lapse all analysis functions are disabled to prevent any possible interruptions in the communication These commands will be enabled when the Acquisition is finished stopped or paused When the acquisition time is reached the program stops automatically Report flep 1 This command will open the Report Output window F3 Report Output Advanced Report Options Group Statistics Excel csv Text txt ME Iw StdEmor Std Dev m NU Output format Rows C List P god Generate Cancel 2 wimicrotrackerspOn 29 22052013 1238 Bin size min At this window it is possible to configure the file format of the experiment s report The report can be generated in TXT plain text format or in CSV text format which can be loaded by Microsoft Excel or almost any other spreadsheet application The output format section allows choosing if activity time block will be presented in columns rows or as a representation of the sensors array Also the size of the time blocks to be reported In the Group Statistics section it is possible to choose which statistics the report will contain Standard Error Standard Deviation and group size N Top plot Activity Counts The top plot shows e Number of samples being acqu
3. 4 Proyecto cacac SELECT PROJECT TO LOAD Cancel Saving Data and modifications in the current project select Save and confirm Yes to upload values into current project Config sub menu The Config sub menu allows choosing microplate format acquisition lapse and 17 locomotor activity detection algorithm m Acquisition setup Groups Well Format w384 Apply Please select the appropriate configuration for your Ou tput Acq Lapse 5 min experiment Tools DSP Method 1 Threshold Avrg Default amp gar amp Liquid Well format Microtiter format This option configures the type of well to use After selection the Go button loads the microplate file setup 384 wots microplate S6well microplate flat bottom W906 w96 flat S6well mucroplate U bottom W965 LU or W96 in old versions 24well microplate flat bottom W384 W24 Discontinued for incompatibdities with some microplate trades 6 and 12 wells plates are also supported NOTE PLACE THE CORRECT ACRILYC ADAPTER ACCORDING TO MICROPLATE FORMAT SELECTION Acq Lapse Acquisition time This option configures the duration of the data acquisition for each run Maximum 32000 minutes DSP method Activity detection algorithm There are two Digital Signal Processing algorithms available Default 1 18 O Threshold Binary First reported Algorithm With filters 1 u 1 u 0
4. 23 saved then the Channel Signal option will plot in the screen the activity of the all the channels asociated to the selected well separetly NOTE The data will be loaded to memory in 25k sample blocks It is possible to navigate through the run moving the slidder Page changing could take some seconds while the data is loaded sample Report Group Activity Channel Signal Analyze Threshold 1 8 SNA Mode 0 l Page 1 10 Also it is possible to Export the data that is being displayed to Text ASCII or Graphic Windows Paint file by clicking the Right mouse button on the graphic 24 Analyze 100 Time min sii Ais rane teet Report Group Activity Channel Signall Page 1 10 This option performs a post run threshold calculation grey line which usually provides more accurate noise and activity detection than the on the fly algorithm used during the run At the bottom of the graphic the numbers indicate how much activity exists in the corresponding time period for each channel in the selected well To the right of the Analyze the size of the threshold and the detection method can be selected NOTE CHANGING THE TRESHOLD LEVEL WILL GREATLY ALTER THE RESULTS SO BEFORE SETING THIS PARAMETER PLEASE CONTACT PHYLUMTECH PERSONEL FOR FURTHER ASISTANCE 25 Test DEVICE Screen This screen can be used to test the working order of each one of the signal channels of the device It can be acc
5. explaining so will be displayed on screen Ops Data Writing ERROR reg 130 Check COM and Try again To correct this problem the connection of the equipment to the computer and to the power supply should be checked If neither one of this items fixes the problem then the WMicroTracker support team should be contacted 27 ares MEME M NINE Power supply 15 9 8 5 Volts Consumption 15 Wats iore OE infrared wavelength 1 880 m Microbeam power 125 i m Microbeam size 150 m Microbeam dispersion angie i16 Grad ee MNT pp COMMUNICATION PROTOCOL protocol CSB or R 232 USB adapter Configuration 115200bps 8bits 1stop np Maximum distance between PC 4m and equipment 28 If you have any comment or problem just contact us to info phylumtech com Software and system updates available at www PhylumTech com 29 30
6. 15 This tab is used to set acquisition parameters experimental groups and microplate format PROJECT 33 Biological Replicate Groups O00 Group 001 Group1 n02 Groupe 003 Group3 004_Group4 005_Group5 Free channels Channel AIO PROJECT Rename Load y Save Parameters and Configurations are saved for each new Project and maintained 16 for every run of said project until the user changes them parameter changes does not alter raw data of previous runs Data for each run is stored in the computer HD in separate folder within the project folder Projects are identified by an ID number automatically assigned plus the name assigned by the user In this way subfolders will be saved into the main application folder starting with p00001 for project number one p00002 for project two and so on All data related to a specific project will be saved into these subfolders For the first time the program is started the default project number p00000 New Projects Select New in the Setup screen If Save is pressed The system will ask you to upload current project selecting No will also generate a new project Change Project Name Select the Rename option and enter the new name Reading an existent Project When the Load button is press a projects list will appear It is possible to select the required project clicking on it Rename Load Save PROJECT
7. Control 21 OFFLINE Screen This tab allows reloading old projects reading saved data and exporting it to text and graphic files First it is necessary to select the Project to read and the desired experiment Project lt Back gt 24072003 1231 24072003 1306 24072003 1351 Once loaded the experiment it s possible to plot the data pressing Group Activity or selecting the well number The activity will be grouped by 30 minutes blocks 22 Well C10 294 Time min 60 30 Report Group Activity Channel Signal Analyze Threshold hs SNR ModeO v Page Project pODOT 7 Javier 15 7 lt Subproject gt 15072011 1707 Corrida 1 010 32w 12mM H SOME o o e ees rg w36f Acq Lapse 480min Groups D3 DOO 21 5w OmMH202 gt 001 21 5w 1 5mM H202 gt 002 21 5w 3mM H202 Sus l na D10 el lt l 260720111303 H202 015 48w 6mM H202 gt 015 48w 12mM H202 017 48w 24mM To plot the activity Activity Group and Channel to draw should be selected It is possible to Export the Graph pressing the Right mouse button on the graphic The Graph can be exported as an ASCII file or as a Windows Paint image Report Button This command will open the Report Output window See Main Screen Channel Signal It is posible to save real time data from every run see Output sub menu which will retain all the signal values stored for each channel If real time data has been
8. Mmicrotracker designplus Produced under license of CONICET Argentina 2013 For research purpose only Not for human diagnostic Data acquisition system WMicroTracker Hardware version WMTKO9 RO01 Software version WMTK V2 5 Rev A 2013 This product is protected under international patents owned by Argentinian National Research Council CONICET P20060105084AR PCT IB2007 054628 US12515723 amp EP2086408B1 All rights reserved Any partial or total copy is not allowed and will be subjected to law penalties Product provided to use As it is Not modifications allowed without CONICET permission When the client acquires this product the client understands and accepts these rules For research purpose only Not for human diagnostic 2013 Made in Argentina WMicroTracker DATA ACQUISITION SYSTEM User Manual ooftware version WMTK V2 5 Rev A 2013 http www PhylumTech com 2 INDEX Preinstallation requirements Overview Introduction About WMicroTracker How it Works Some system characteristics Connection schematics Packing list Software description Minimum requirements Software installation Starting the application Main screen Setup screen Off Line screen Test DEVICE screen Specifications O O COO N O O Ci a C C A N N N oc o O N Oi O O Thank you for acquiring our product Please read carefully this manual before proceeding and save it for future reference Equipment i
9. croplate format adapters 384 wells 96 w flat bottom 96 w U shaped bottom Acquisition Software CD ROM Software installation Minimum requirements IBM PC compatible CPU gt 1 0GHz gt 512Mb RAM gt 200Mb free space on HD gt 10Gb free HD space recommended for real time data saving MS Windows XP Windows 7 and Windows 8 USB port Screen resolution optimized to 1024x768pixels minimum 800x600 gt Installation 1 Insert WMicroTracker CD or download installation files from PhylumTech website www PhylumTech com 2 Connect the provided USB cable to the device and to a free USB port on your computer and execute USBDriverlnstaller exe from the USB driver folder 3 Windows XP Install the WMicroTracker acquisition Software from the Windows XP Windows 7 Extract the ZIP file from the wmicrotracker win v25 folder into c V and execute Reg MSComm32 Ocx Windows 8 Extract the ZIP file from the wmicrotracker_win8 v25 folder into c V The following files will be copied to the HD Installation package Application for Installing the setup Installation package setup lst oystem installation directives Only for downloaded version System files w96f dat 384 channels setup for 96well flat bottom plate w96u dat 384 channels setup for 96well U shape plate w384 dat 384 channels setup for 384well plate ace Runtime files Runtime for programming langua
10. essed through the File menu w lt W Micro Tracker gt Acquisition Software File Help Settings Advanced d Test DEVICE Exit Setup Before starting a test it should always be checked that there is no plate in the equipment and that the door is properly closed After confirming the initiation of the test the Top Plot of the Main Screen will turn into a schematic of the sensor array displaying the received signal of each sensor the color of each sensor displays the intensity of the signal darker colors for lower signal and brighter colors for higher signal It is not necessary for the signal of all the photoreceptors to be similar the system performs an automatic calibration before and during every run to determine the appropriate rate between IR beam intensity and photoreceptors sensitivity 26 nDozzmor x rgommoogr Report Bm size nin At this point the system will begin a series of tests where it will set the microbeams emitters to maximum minimum and medium levels for each sensor If the system is working properly the color of the sensors on display should change accordingly NOTE It is possible to manually assess the working order of the sensors by opening the equipment door during the test By doing so the tray of the device will block the IR beams turning the received signal to a minimum If there is a communication problem between the equipment and the computer a message
11. ge communication protocol library All this parameters are set by the Main Application there is no need to access them directly For detailed procedure check System Check Ups technical bulletin Starting the application When the application is started the program checks the equipment communication and loads the setup file if one has already been recorded If any problem is detected a message box will appear If no WMicroTracker equipment is connected the system will report a COMM PORT ERROR and ask for the correct COMM PORT pressing enter at the error pop up will access the offline mode Mm microtrac Fast Throughput Acquisition System lt 2010 c gt V2 2 rev beta gt gt STARTING Reading Configuration IMPORTANT It is recommended not to have other programs running in parallel in the computer while performing the acquisition since it could interfere with data communication speed and DSP data processing MAIN Screen The main screen is the first screen showed when the program starts in online mode 10 Tools c amari LA F fe Au 3h33 Laghi Dart Enabled Channel A Toon ram hr Cyce Pua OFF d In this windows the following buttons exists Play Pause y Stop Button Play b Starts the data acquisition lapse A name for the current run will be requested for future reference Acquisition lapse is configured in Setup Config
12. ired in the current time lapse e Temperature e Selected Channel microbeam activity e Selected Well activity e Experimental group average activity 12 The algorithm used to detect locomotor activity must be selected in the Setup tab When the acquisition finishes it is possible to view the results using the command Report or working in the offline window M5 ampzzbbl CHO Activity GO_ 21 50 mb Hz 2 B epar k If more than one microbeam channel crosses through one Well then the mathematical average of the channels will be calculated Group activity is calculated as the average of the activity of the wells in that group Bottom plot Raw data The bottom plot shows the current Raw data for the selected channel sensor red line versus time The locomotor activity detection threshold blue green line is drawn below the Raw data If the signal falls below the threshold it increments the activity counter at the top plot 13 p P Mata Hat nN F gt Threshold Time Zoom It is possible to Zoom in and out the plot to view the data with further detail Channels and Group list Channels and Wells are sorted by experimental group These Groups are generated from the Setup tab The Well channels are selected for display by double clicking on the list or by pressing Enter A a Selected Well channel 000 cti sin h202 Experimental Group Well Channels into the G
13. nstallation and setup requires the following items 9V to 12V DC switching power supply with 1 5 Amps output provided USB cable and O S drivers Provided IBM PC compatible with the following minimum requirements Pentium II processor or above gt 1GHz clock 512Mb of RAM memory 1 USB port available DVD ROM unit optional Windows XP 32bits or higher operative system At least 200Mb of free HD space Workbench space required for equipment installation 22cmx28cmx9 1 cm Ambient free of vibrations and dust Optimal temperature range 10 to 28 C Preferably low humidity lt 50 Due to customs restrictions in some countries the system might not come with the power supply In those cases PhylumTech will provide de power supply from a local distributor This range is for equipment functionality only biological samples might have unique temperature requirements Introduction Locomotor activity in animal models is a common parameter in disease studies and drug activity quantification This readout has been widely used in Parkinson Alzheimer and Huntington research as well as a wide range of metabolic disorders neurotoxicity aging circadian rhythms and novel drug discovery About WMicroTracker WMicroTracker provides the capability to measure in an easy fast and highly reproducible way the locomotor activity of small animals cultured in microtiter plates This system is meant to be used in High Throughpu
14. roup Note When more than one microbeam crosses though one well e g when 96 wells flat bottom or 24 wells plates are used then a sub index will be added to the Well name 0 1 2 3 etc This sub index corresponds to each of the microbeams crossing the well 14 Tools Submenu Tools options allow the user to adjust system functions AutoCalibration tool Tools Ic elegans L4 lw Auto Calibration W Auto ero Pere Auto Calibration and Auto Zero allows to perform experiments directly using a well plate with animals and test solutions without blank plate measurement This option automatically calculates the best sensors configuration and the appropriate detection threshold Briefly the system applies a short algorithm to adjust detectors to linear range and measures high frequency noise level to calculate the best threshold for animal movement detection This setup is optimized for C elegans worms and similar size organisms 0 1 to 1mm long Lighting Control Tool Light Ctrl Enabled ON s h OFF 21 h OFF Light Control is used to set fixed Light Darkness cycles for circadian rhythms experiments Temperature Control Tool Temp Ctrl Enabled 20 0 t SET OFF FRIO Temperature control is used to set a fixed system temperature for Peltier cooled equipment This options are not available for all of the WMicroTracker range SETUP screen Experimental Configuration
15. t Screening assays to evaluate the biological effects of potential compounds drugs RNAi morpholino as well as mutants studies in the model organisms Caenorhabditis elegans worms Danio rerio zebrafish larvae Xenopus laevis tadpoles Anopheles sp mosquitoes and similar sized animals On request software may be customized for larger size animals in 24 12 and 6 wells plates How it works WMicro Tracker detects the animal movement through infrared microbeam light scattering Each microtiter well is crossed by at least one infrared microbeam scanned more than 10 times per second Micro Controller f Circuit The detected signal is digitally processed to calculate the amount of animal movement in a fix period of time Some system characteristics 384 independent and simultaneous channel readouts Automatic calibration real time data acquisition and monitor function 384 and 96 wells microtiter plates adaptors also possible to use 6 to 24 wells plate on demand Different animal models capability C elegans Drosophila sp Danio rerio Xenopus sp tadpoles and similar sized organisms Phenotype automatic detection customization on demand Low current consumption 0 5Ampers and insignificant heat emission Connection schematic RS232 Port COMM USB Port Power supply LED The system includes the following accessories Microplate 9V dc 1 5Amp reader switching Power system Supply USB cable y Mi
16. wever if the Save Real Time option is enabled all the data will remain separated in different files to enable future analysis CLEAR LIST Button Removes all channels from the group gt button Adds the selected channel to the current group Clicking and dragging the cursor over the wells on the plate schematic below will also add them to the group NOTE Each well can only be assigned to one group and all channels associated with that well will be assigned to that group lt button Removes the selected channel from the current group Right click on the wells from the plate schematic below will also remove them SET This drop down menu has a list of preset group configurations described by the amount of rows and columns that each group will occupy on the plate The 20 preset will be loaded upon selection after clicking the Go button NOTE ALWAYS REMEMBER TO SET THE CORRECT WELL FORMAT IN THE CONFIG SUB MENU BEFORE SETTING UP THE GROUPS Output sub menu The Output sub menu allows defining which data is going to be stored in hard disk files Co nf i g File Output Groups Working Folder C vMicrotrackerpO0016 Save Counts minute res zj Save Real time data ES Tools sub menu The Tools sub menu allows defining which tools will be shown in the main window Config Tools G roups v Calibration Control Output Light Control Stasis E Temperature
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