Commit 0e5dce13 authored by Aliaksandr Halavatyi's avatar Aliaksandr Halavatyi
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Installation guidelines

parent 09728480
# Installation
### Automatic Installation via Fiji update site (preferred, requires internet connection)
1. Start **Fiji**
2. Run *Help -> Update...* from the main Menu.
3. Press *Manage update sites*
4. On the bottom of the list add the URL of the **AutoMicTools** Fiji update site: *https://sites.imagej.net/AutoMicTools*
1. Press [Add Update site] and in the line appeared on the bottom of the table type the URL in the **URL** column.
2. Tick the corresponding checkbox in front of this item.
5. Close *Manage update sites* dialog
6. Click *Apply changes* and wait until new dependencies are downloaded
7. Restart **Fiji**.
### Manual Installation
1. Install the**AutoMicTools** library and its dependencies of by copying following files to the ***Plugins*** subdirectory of your Fiji installation:
1. `AutoMicTools_-x.x.x.jar` from [this page](https://git.embl.de/halavaty/AutoMicTools/-/releases) (use the latest available version, unless another version is recommedned to be compatible with one of AutoMicTools extensions libraries).
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/)
......@@ -24,9 +24,15 @@ To perform these and other types of complex fluorescent microscopy experiments i
Customisable workflow procedures trigger execution of image analysis functions. Information about all acquired images, identified regions and decisions made by the system is stored in a special data structure that is exported from the software as a text table. Our visualisation module imports this table and provides a GUI to efficiently navigate through the acquired datasets and show segmentation results as overlays on acquired images. The data is also used by post-acquisition analysis procedures to import raw images and link quantifications to corresponding image and ROI files.
# Documentation
- [Installation guidelines](./Documentation/manual.md)
## Contributors
Aliaksandr Halavatyi (ALMF, EMBL): development and support.
- Aliaksandr Halavatyi (ALMF, EMBL): development and support.
- Manuel Gunkel (ALMF, EMBL): development and support.
## Related projects
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