User:Nadiezda Fernandez-Oropeza/Notebook/Notebook/2011/06/21

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Data analysis cheat sheet

 * This entry contains a set of steps to take when analyzing the data of the gliding motility assay. This is not intended to be very informative, but to serve as a personal reference. The following programs were written in LabVIEW 7.1, by Larry Herskowitz (KochLab).

Temperature control
Hit OK at the pop up window. On the Communications section, click connect. On Controller Options, click OK. Then, browse for the text file just created and save. Manually set the scale on the graph for a better view. Keep in mind that the control temperature has to be at 33.5 °C. The temperature controller has to probes, one connected to the upper part of the objective (shown by the green line), and the other one connected to the lower part of the objective (shown by the yellow line).
 * 1) C\Temp Local\MT Programs\Temperature
 * 2) *Create a new text file with the date. Sample: Temp2011_06_20.txt
 * 3) C\Temp Local\MT Programs\Temperature Controller

Camera

 * 1) C\Temp Local\MT Programs\Camara.vi
 * 2) Turn the camera switch on and click on Run.
 * 3) The following values have to be set:
 * 4) *Capture rate: 0.2
 * 5) *Total frames for png, set to zero for no limit: 600
 * 6) *Gain: 150
 * 7) *Exposure: 0.1
 * 8) Name the file, and the path will automatically be given.
 * 9) Click the big red bottom to record.

Tracking
The tracking can be done automatically, or individually. The following are the steps for automatic tracking: C\Temp Local\MT Programs\Tracking.exe Click on Run On the overall directory, select the folder with the set of data to analyze. For the template file part, select the following: C\Movies from Live Feed\Tracking Templates\convoluted template 2.png GO

Analysis
C\Temp Local\MT Programs\Analysis.exe The program is a little complex and it will take some time to master all its properties and features. The part we need so far is the array of pools. Click on “Edit these values” and a window will pop up. There, one has to upload the folder with the data we want to analyze and we can string any name to the results. Once that is ready, just activate the tracking bottom that is placed next to the smoothing Gaussian parameters.

Velocity Average
C\Temp Local\MT Programs\Peaks.exe On the parameters section, upload the folder with the data we want to analyze and change the number in the “Pattern matching cluster section.” Instead put the number that goes in front of the file name in the directory array. Finally, press Go.

Unfortunately, there isn’t any indicator that the program has finished analyzing the data. However, one can make sure by going to: \\controller\webpub\files\data\MTD  and looking for the folder with the correct date, if that folder contains the peak v time.dat file, then the processed is finished.


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