Commit 7375f51a authored by Timothy Jessen Fuqua's avatar Timothy Jessen Fuqua
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parent 82258d68
......@@ -24,9 +24,15 @@ The purpose of this software is to automatically locate and carry-out high-throu
6) Each job will be loaded into the microscope. To view a job in Zen, simply click on the button "Macro-->Zen" in the JobSetter window. Changes can be made to the job and will be saved by clicking the "ZEN-->Macro" button in the JobSetter window.
7) Return to the MyPiC window and select the folder icon in the bottom right corner.
![alt text](img/img05.png "Title text")
8) Open the file "PipelineConstructor.ini" - these are the settings for the pipeline.
9) Navigate the microscope to the well in the top left corner of the microscope slide and make sure that it is relatively in focus at 5x magnification.
10) In the MyPiC window, select the "Default Positions" button and click the "Mark" Button. The user may have to change these settings depending on how the sampels are mounted on the slide.
![alt text](img/img06.png "Title text")
11) In the MyPiC window, select the "Saving" button
12) Select the "..." button and create a new root directory to store the acquired images, subdirectories, and imaging settings.
13) In the "Base File Name" enter a unique ID name for the run. It is very important that you change the name of this each time you run the automation.
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