1、EOD Machine General Instructions for Use(Anya Goldina, 2008)III. Calibrating tanks1) Why is it necessary to calibrate tanks?To ensure that all tanks record EODs accurately and consistently, tanks need to be calibrated on a regular basis. Because recorded amplitude and frequency are sensitive to chan
2、ges in water temperature and conductivity, it is imperative that you and the EOD machine can account for these changes by calibrating the tanks anytime you change recording parameters. Also, since the electric field changes depending on water levels, once a tank is calibrated at a certain water leve
3、l, try to maintain the tank at that level throughout the duration of your experiment (you can do this by marking the original water levels with a piece of tape, as the water evaporates add a little at a time.)2) When is it necessary to calibrate tanks?a. When you are starting a new experimentb. When
4、 you change either the conductivity or water levels of an existing experiment.c. When you put in new fish into an existing experiment (increasing sample size)d. Anytime you change anything about the physical aspects of the tanks (i.e., electrodes, ceramic tube, mesh partitions) that would require ta
5、king some aspect of the tank apart.3) Important things to know BEFORE using the calibrator. The calibrator is VERY fragile. You must treat it as gently as possible! If it breaks, immediately tell Phil. If you are unsure about using it, ask someone in the lab to help you. However, accidents do happen
6、, and if the calibrator does break it is your responsibility to fix it and make sure that it works! When you are calibrating tanks, no data will be collected for the period of time it takes you to calibrate. Therefore, if you are sharing the EOD room with someone else, it is important to coordinate
7、calibrating times. When you finish calibrating, restart the EODrecorder12, otherwise the new information from the calibrator will not be integrated into the program and you will not be able to collect any data. Simply resuming EODrecorder12 by switching to Run after Pauseing, will not work! Only cal
8、ibrate tanks when the water level, temperature and conductivity meet the specifications of your experiment. There is no point at calibrating a tank at one condition and testing fish at another.4) Calibration Protocol for tanks in the EOD room(Anya Goldina, 11 Jun 07, adapted from V. Salazar (4 Oct.0
9、1) and J. Herrick (2 Jul 02)All MATLAB commands are italicized a. Select MATLAB icon on the desktop to open a windowb. Type calibrator the calibrator window will openi. If you or someone else is collecting data, click Pause in the EODrecorder12 window.ii. The calibrator window should have 4 buttons
10、(calibrator, tank, calculate and offset). If you dont see all four, close and reopen the program.c. Take the part of the calibrator apparatus that has a transformer (blue box) connected to a BNC cable and connect the cable to the Out-1 of the RP2-#1. This portion of the apparatus should remain plugg
11、ed into the RP2-#1, Out-1 regardless of the tank that you are trying to calibrate.d. In the EOD room, install the calibrator apparatus inside the tank of interest. (NOTE: be very careful with the calibrator; if you break any of the fine glass tubes, Phil will kill you!)e. When installing the calibra
12、tor, make sure that the two metal balls are to your right and that they are aligned vertically with the ceramic tube. Also, make sure that the calibrator itself is centered with respect to the ceramic tube.f. Connect the blue cable on the calibrator to the Type 1(tank) cable of the tank of interest.
13、g. At the computer, on the Calibrator window, select the tank # to be calibrated and the gain of the amplifier.h. Then select calibrator. Record the given value in a notebook.i. In the EOD room, remove the blue Type 1 cable from the apparatus and reconnect it to the tank. Leave the calibrator in the
14、 tank.j. At the computer, in the Calibrator window, select Tank then Calculate. k. Two values will come up: the calib value and the offset value. Record both values in your notebook.l. When all the tanks have been calibrated, click on Edit setup.m in the Calibrator window.m. Enter in the new calibs
15、values for each tank that you calibrated, then enter in the new offsets values. Make sure to enter date of calibration and person doing the calibration.n. Go to FILE and save and close the current file only! (the lower ) If you close the top one, it shuts down the program!o. Select close on the Cali
16、brator window if you are done for the day. Unplug the BNC cable from the RP2 and plug back in the original cable. p. If you need to calibrate other tanks, go back to step c and repeat.q. For the new calibration values to be uploaded, restart eodrecorder, by typing in eodrecorder12. If the eodrecorde
17、r has been paused while you were calibrating, close the program and restart by typing in eodrecorder12.r. Before leaving, verify that the EOD machine is collecting data from tanks where you or your labmates have fish.Troubleshooting:1) When I start the program calibrator, not all buttons show upa. R
18、estart calibrator2) Calibration values are sporadica. Make sure that your conductivities are within the same range between tanks.i. If you are running different species that require different conductivities, your calibration values will also be different. Higher conductivities will give you higher c
19、alibration values. However, all values should be below 1.b. Make sure that neither the XLR connectors nor the BNC connectors are touching each other or the copper-mesh cage around the tank. Metal-metal contact will interfere with the calibrator. Try putting a dry cloth or towel underneath the metal
20、part of the electrodes and calibrator.3) Calibration values are greater than 1a. You have tank (type1) and tube (type2) cables mixed up. Recalibrate making sure that you connect the calibrator apparatus to the actual tank cable, NOT tube. The same applies for reconnecting the actual electrodes back
21、to the cables.4) My conductivities are right, and my cables are connected properly, but I still cant get a good calibration value on some tanks.a. It is possible that one of the tank electrodes is bad. A simple fix is to change the electrodes. If there are no spare electrodes, take the existing pair
22、 out and see if the wire needs to be re-soldered (refer to the electrode protocol.)IV. USING EODRECORDEREODrecorder12 is a program written by Philip Stoddard and Michael Markham that allows you to record EODs of pulse and wave type electric fish continuously for extended periods of time. To start us
23、ing the eodrecorder you need to have the following items:1. Calibration and offset values for each tank that you intend to use (see calibration protocol above)2. Assign names to the fish whose signals you will be measuring.a. Names are assigned based on Genus, Species, Sex and numberi. For example1.
24、 bpm025 stands for Brachyhypopomus pinnicaudatus male, number 252. gcx033 stands for Gymnotus carapo, sex unknown, number 33.3. To find out which number to give your fish, look at the bottom of the dry-erase board, find the abbreviation for your species and choose the next number up.3. Know whether
25、your fish is pulse or wave. 4. Assign a number to your experiment. As in fish numbers, look at the dry-erase board to see the last experiment number that was used and choose the next number up.USING EODRECORDER12 (All MATLAB commands are italicized)I. Double click MATLAB icon on the desktop to open
26、MatlabII. In the command window (largest window) type edit setup and press Enter a new Editor window will open.III. CREATING FILES/ FISH FOR RECORDINGScroll down until you see 12 lines “fish1= ;fish 12 = ;”a. These represent the 12 tanks in the EOD room into which your fish will go (i.e. fish1 is ta
27、nk 1, fish2 is tank 2.)b. Type in the name of your fish next to the tank number in which you will put your fish. c. Make sure that each name has single quotes on each side of it bpm001i. If the quotes are not there, the fish name will be black.ii. If you are missing one quote, text will appear red.
28、d. If no one is using the first tank, the file name of tank1 should be dummy, it should look like this: fish1 = dummy. Without this, the eodrecorder will not work.IV. SETTING GAINS Scroll further down until you reach a section that says gains (1).gains (12). Here you will set the gain at which you n
29、eed to record your fish. The gain number should reflect the gain setting of the amplifiers of each tank from which you are recording. a. The amplifiers are located to the left of the computer. Each amplifier has a number on it that corresponds to the tank in the EOD room whose signal it is amplifyin
30、g. b. Once you have located the correct amplifier, check the setting of the gain. (It is usually set at 500).c. Compare that setting to the one noted in the setup file. i. If the setting is correct, you dont have to do anything.ii. If the values dont agree, type in the correct value next to your tan
31、k, followed by a semicolon1. Note, no quotes are needed here.V. RECORDING WAVE vs. PULSE TYPE FISHScroll further down until you reach a section that says tanktype (1) . tanktype (12). In this section you will tell the eodrecorder whether it is collecting data from a pulse a wave-type fish. a. While
32、you can record EODs of wave and pulse type fish simultaneously, tank types must be in pairs. Tanks are paired in order, tank1 is paired with tank2, tank3 with tank4 and so on. Therefore, if in tank 1 you are recording from a pulse fish, you cannot put a wave fish into tank 2. In such scenario, you h
33、ave to put a wave fish into any of the other available tanks that are not paired with “pulse” tanks. b. Next to the corresponding tanktype type in 1 if you have pulse fish and 2 if you recording wave fish. i. Thus, if you recording the EOD of one wave fish in tank 1 and another pulse fish in tank 4,
34、 your command lines should look as follows: tanktype(1) = 2; %wavetanktype (2) = 2; %wavetanktype (3) = 1; %pulsetanktype (4) = 1; %pulseii. Note, even though, I only have fish in two tanks, all four tanks are assigned a pulse or wave command.iii. Signal type designation should be followed by a semi
35、colon. iv. Any text that is preceded by a percent sign % , is not read by Matlab and can be used to make notes or reminders for yourself. VI. SETTING CALIBRATION VALUESSee calibration protocol aboveVII. UPLOADING NEW INFORMATION AND STARTING YOUR EXPERIMENTa. Save all your information by choosing Fi
36、le (upper left-hand corner) and click Save.b. Close the Editor window.c. In the Matlab command window type eodrecorder12i. A new window will open that has 12 squares on the bottom, for each tank in the EOD room.ii. The upper half of the window should have a Threshold setting, a larger window in the
37、middle and a History window on the right.d. If you already put your fish in the tanks, then within a few seconds an EOD waveform should appear in one of the bottom windows corresponding to the tank in which you have fish.e. If you have not put your fish in the tanks yet, go ahead and do so now. You
38、should see the EOD signal in one of the window.VIII. SETTING THRESHOLDSIn order to be able to record the EODs of your fish accurately, you need to set the thresholds as tight as possible. Setting thresholds tells the eodrecorder when the fish is centered in the tube and triggers the tank electrodes
39、to record the EOD. If you set your thresholds too high, then you might not record any data. However, if your thresholds are too low, then your data will be noisy, because any movement of the fish will trigger the eodrecorder. Here are a few steps to help you set your thresholds:a. Once you put your
40、fish in the tank, wait until it enters the tube.b. Once you are sure your fish is in the tube, come outside and look at the oscilloscope.i. Make sure to select the proper tank by turning the dial that says “Select” below the oscilloscope until the green light is right below the right tank number.ii.
41、 Look at the signal on the screen. The signal should be in two colors, pink and blue. iii. Note where a yellow line is in relation to the signal- this is the threshold line. 1. The threshold line should be at the tip of signal. If it is too high, then you will not be able to record anything.2. If yo
42、ur line is too low, then the signal will be too noisy. iv. You can adjust the threshold within the eodrecorder12 window:1. In the top left corner that says Thresholds, choose the tank to be adjusted.2. Increase or decrease your day settings, by pressing + or signs and then clicking Apply. There are
43、two ways to tell that your new thresholds have been uploaded:a. In the History window “ thresholds changed locally and uploaded” should appearb. On the oscilloscope, the yellow line will move in the direction of your adjustments.v. Once you set the daytime threshold settings, adjust the nighttime th
44、resholds.1. A general rule for setting nighttime thresholds is that nighttime values should be double of the daytime settings. Thresholds need to be higher because the fish move during the night and if settings are not tight enough, they will trigger the eodrecorder everytime the fish is close to th
45、e tube electrodes, and not when they are centered within the tube. a. You might have to tweak these values to make your data as accurate as possible, but this is good beginning for the first night.IX. VIEWING THE SIGNALYou can view the data you have collected by using eodshow. This is a program for
46、viewing how the EOD of your fish changes over a period of time. You can also see different parameters of the EOD signal (amplitude, frequency, duration, etc.)a. In the Matlab command window, type eodshowi. A new window should openii. On top of the window you should see a button that says D:data this
47、 is where these data are accessed from.iii. To your right there are two buttons:1. Update file list click this when you want to view a signal of a fish you have recently started recording2. Update plot click this when you want to see recent changes in the EOD of your fish3. Use the scroll down menu
48、to choose the fish whose signal you want to see.4. Once you choose your fish, choose the EOD parameter that you want to see.X. SAVING YOUR DATAIt is imperative that you save your data at the end of every experiment and also back it up on the lab server!a. While you run the experiment your data is co
49、llected on the D drive.i. You can find it on the “Shortcut to data” folder on the desktop.b. For every fish that you run, eodrecorder will create 3 files:i. For example, 1. for fish bpm666, eodrecorder will create bpm666, bpm666.ana and bpm666.rawii. At the end of your experiment, you need to save all these files.c. To save files:i. pause the EODrecorder12ii. Open “Shortcut to data” file on desktop and locate your filesiii. Open “T Drive (data on server)” shortcut, also on desktop1. Open EO
