Malaria-Detection

This is a project to Detect malaria. The interactive graphical user interface (Napari plugin) developed allows you to: Reconstruct high resolution images from low resolution ones, and to retrieve phase information using Fourier Ptychography Microscopy, segment red blood cells using (classic,advanced) algorithms, classify cells into healthy/infected, visualize the results, and allows for individual control of blood cells at the various imaging, processing and classification steps.

Setup

1- You should first create a virtual envirement (in my case I used conda): conda create -n yourenvname python=3.8.10 anaconda Then activate the envirement: conda activate yourenvname

2- Install Napari:

https://napari.org/tutorials/fundamentals/installation The editable mode was used (as Napari is in an alpha stage, it may be better to stay in touch to new changes) :

git clone https://github.com/napari/napari.git
cd napari
pip install -e .[all]

3- Try to launch napari to check if it works, by running in your terminal: napari

A new window should appear showing the Napari default window, if not please refer to the Napari website cited above.

4- Then you should install some packages: Stardist: pip install stardist Cellpose: pip install cellpose Tensorflow: pip install tensorflow opencv: pip install opencv-python LightPipes: pip install LightPipes scikit-image: pip install -U scikit-image

5- Then you should set the path in Terminal to : Malaria Detection/Malaria-Detection/cell_annotator/, where the file setup.py is located, then run : pip install .

6- After that, run in terminal: napari (Napari window should be closed before running this)

7- In the menu bar (of Napari window) go to plugins --> napari-cell_annotator, where you should get the list of plugins (Image_preprocessing, segmentation, Image classification, ...). To open a plugin click on its name in the list.

8- In case you didn't find napari-cell_annotator in plugins --> napari-cell_annotator, you can even:

• Solution 1: Go to plugins --> install/uninstall plugins.. then check if in installed plugins list you have napari-cell_annotator (where the check box next to napari-cell_annotator should be checked, if not check it and close this window then go to step 7.

• Solution 2: Close Napari window, then set the path in your terminal to where _dock_widget.py is located, then run : pytest _dock_widget.py this will allow you to visualize the errors you have ( which are generally related to a package that you should install). If so, install the needed packages then go to step 5.

For a better undrestanding of how to use the different plugins, please refer to the file : Malaria_detection_Plugin_Documentation. For more explanation about the work (technical aspects), it can be found on the papers folder.