Commit 05cdb720 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi

Update manual.md with installation details

parent 9585d76f
# 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.
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 LSM 780 or Zeiss LSM 880 confocal microscopes.
# Installation
1. Download and install [**Fiji**](fiji.sc) on microscope computer (typically Windows 64-bit version is required).
2. Install **Fly_Embryo_feedback** library containing plugins imalementing the developed piupeline. Download the latest version of `Fly_Embryo_feedback-xxx.jar` from [here](https://git.embl.de/grp-almf/feedback-fly-embryo-crocker/-/releases]) and copy it to the ***Plugins*** subdirectory of your Fiji installation.
3. Install the dependencies of **Fly_Embryo_feedback** library by copying following files to the ***Plugins*** subdirectory of your Fiji installation:
1. `AutoMicTools_-1.1.4.jar` from [this page](https://git.embl.de/halavaty/AutoMicTools/-/releases)
2. `reflections-0.9.12.jar` from [this page](https://javalibs.com/artifact/org.reflections/reflections)
3.
Note: later versions of the same libraries can be used. Mentioned versions vere tested for the compatibility with the latest **Fly_Embryo_feedback** pipeline version.
3. Start Fiji.
4. Get additional required dependencies via update sites (requires internet connection)
5. Run *Help -> Update...* from the main Menu.
5. Press *Manage update sites*
6. Tick checkboxes in front of the following items:
- *EMBL-CBA*
7. Close *Manage update sites* dialog
8. Click *Apply changes* and wait until new dependencies are downloaded
4. Restart Fiji.
5. Download **MyPic.lvb** macro file to your microscope computer from [here](https://git.embl.de/grp-almf/mypic)
# Quickstart
1) Launch the Zen Black Software.
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