Commit 5faadb95 authored by Timothy Jessen Fuqua's avatar Timothy Jessen Fuqua
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Update manual.md

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# Overview
The purpose of this software is to automatically locate and carry-out high-throughput imaging of *Drosophila* embryos. Using Zen Black and Fiji / ImageJ, embryos can either be selected manually or automatically and imaged on a Zeiss 780 or 880.
# Installation
# Quickstart
1) Launch the Zen Black Software.
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# Manual Embryo Selection
1) Follow the directions from the Quickstart section of this manual or run the protocol with your own settings.
2) After the second job, TR2 is run, a dialog box will appear. DO NOT CLICK on this box until you have selected the desired embryos.
![alt text](img/img/13.png "Title text")
An image will open in a Fiji / ImageJ window. Select individual embryos with the left-click on the mouse, followed by pressing “t” on your keyboard to add the positions to the ROI Manager.
3) When all the embryos are selected, press the “OK” button on in the Select Embryo Positions dialog box.
4) Repeat these steps 1-3 for every well. After embryos positions are manually selected for every well, the microscope will begin the automated feedback imaging.
# Changing / Modifying Job Settings
# Viewing data using the Automation Viewer
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