Commit 7170eb6b authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi

manual update

parent 3a93128a
......@@ -4,19 +4,16 @@ The purpose of this software is to automatically locate and carry-out high-throu
# 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. `CommMicroscope-1.1.3.jar` from [this page](https://github.com/ssgpers/CommMicroscope/releases/)
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)
4. Install **Fly_Embryo_feedback** library containing plugins implementing the developed piupeline and its Fiji dependencies via update sites (requires internet connection)
1. Run *Help -> Update...* from the main Menu.
2. Press *Manage update sites*
3. Tick checkboxes in front of the following items:
1. *EMBL-CBA*
3. On the bottom of the list add URLs of reuiqred Fiji update sites and tick corresponding checkboxes in front of these items:
1. *https://sites.imagej.net.Embryo-Confocal-Screen*
2. *https://sites.imagej.net.AutoMicTools*
3. *https://sites.imagej.net.FlyReg*
> To add each URL you need to press [Add Update site] and in the line appeared on the bottom of the table type the corresponding URL in the **URL** column
4. Close *Manage update sites* dialog
5. Click *Apply changes* and wait until new dependencies are downloaded
6. Restart Fiji.
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