Commit 288bbd8c authored by Timothy Jessen Fuqua's avatar Timothy Jessen Fuqua
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Update manual.md

parent e86d85b3
......@@ -34,14 +34,32 @@ The purpose of this software is to automatically locate and carry-out high-throu
![alt text](img/img06.png "Title text")
11) In the MyPiC window, select the "Saving" button
![alt text](img/img07.png "Title text")
12) Select the "..." button and create a new root directory to store the acquired images, subdirectories, and imaging settings.
![alt text](img/img08.png "Title text")
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.
![alt text](img/img09.png "Title text")
14) Launch Fiji / ImageJ.
15) Select the Macro window and (UPDATE THE PATH TO GET TO THE PLUGIN).
![alt text](img/img10.png "Title text")
16) Embryos can be either automatically located by the macro, or the user can select which specific embryos to image at the beginning of the protocol. To allow the macro to identify embryos, select "Automated Embryo Selection". To select the embryos yourself, select "Manual Embryo Selection".
17) Select the root directory created earlier.
18) Multiple dialog boxes will appear. The user may have to change these settings depending on how the samples are mounted on the slide. The given numbers are the pre-settings used during the screen in the publication: (insert link).
![alt text](img/img11.png "Title text")
19) Note: Do not press "Stop Monitor" until complete with imaging.
![alt text](img/img12.png "Title text")
20) Return to the MyPiC macro and click the start arrow.
21) If you are doing "Automatic Embryo Selection", then you are finished. If you are running "Manual Embryo Selection", continue to the "Manual Embryo Selection" section of this manual.
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