Guanine crystal analysis using APOC

Repository of Code used in the Bachelor Thesis "Guanine crystal segmentation and classification imaged in the eye of zebrafish embryos"

• In notebooks the single parts of the image analysis pipeline can be found that helped to develop the workflow libraries (library_crystals, library_crystals_testing).

• In plots are figures and plots shown in the bachelor thesis (enumerated accordingly).

• In tables are dataframes generated from the acquired crystal data which are required for some notebooks to run.

With the help of this code, a napari plugin was developed:

https://github.com/BiAPoL/guanine-crystal-analysis

Instructions how to install and use the napari plugin for guanine crystal analysis

1.) Open your Computers’ terminal window

If you don’t know where it is just use search field and type „terminal“ or „anaconda“ or „conda“

2.) create an new virtual environment named

Type the following command in your terminal window:

• Conda create -n

3.) activate virtual environment named

Type the following command in your terminal window:

• Conda activate

4.) Install package

Type the following command in your terminal window:

• pip install guanine-crystal-analysis

5.) Open napari

Type the following command in your terminal window:

• napari

6.) After napari opened, you can find the plugin under

6.1) Select an image

• File -> open image

Now you have the choice:

6.2 A) Doing all steps manually

• Plugins -> guanine-crystal-analysis -> Normalization, Segmentation, Analyse Image, Classify Objects, Bad Label Exclusion

6.2 B) Doing all at once

• Plugins -> guanine-crystal-analysis -> Analyze Deluxe