Placozoa tracking

This project is about a placozoa that has been cut in its center.

Getting started

Installing the dependencies

To install Python and the required dependencies we strongly recommend to use conda, mamba or pipenv.

Installing conda

Conda can be installed multiple ways. There is no recommendations about how to but one can read there for a likely exhaustive list on ways to install conda.

Note that Anaconda is not necessarily recommended, miniconda might be a better alternative.

Moreover, it is advised to start jupyter notebooks from a shell/terminal/prompt to be able to better see the error messages.

Installing the dependencies

Once conda is installed (or your favorite environment manager), you can create and activate your environment:

conda create -n placozoa
conda activate placozoa

Then, there is a setup.py file with the basic dependencies present within this repository. It means that you can easily install all the likely necessary dependencies using pip. It might be necessary to install it first:

conda install pip

Then, it is possible to install the dependencies, from the placozoa-tracking folder the following way:

pip install .

List of dependencies:

Here is the list of dependencies that will be installed:

• numpy : basic library for array manipulation
• matplotlib : basic library to plot figures
• scipy : one of the basic libraries for image analysis (ndimage)
• scikit-image : one of the basic libraries for image analysis
• scikit-learn : one of the basic libraries for data analysis
• tifffile : library to read and write tiff images
• ipython : interactive python terminal
• jupyter : python notebook
• napari : 3D image visualizer

Road Map

Problems that this software is trying to solve

Understanding better Placozoans wound healing

Objectives

The objectives are likely in order of difficulty but they can be done in any.

It is not expected, whatsoever, for all the objectives to be completed.

• Detecting and tracking the placozoan throughout the whole movie #2
• Quantitatively characterising the shape of the placozoan over time #3
• Detecting and tracking the wound throughout the whole movie #4
• Quantitatively characterising the shape of the wound over time #5
• Building a napari plugin for the detection and tracking #6
• Computing and quantifying the cell flows within the placozoan #7
• Putting in relation placozoan and wound shape with cell flows #8

You can find the roadmap for the project as an issue there.

You should try to follow the objectives but the order is not important (though some milestones are dependent on others).

Objective dependencies

→ #2

→ #4

#2 → #3

#4 → #5

#2 | #4 → #6

→ #7

(#3 | #4) & #7 → #8

Legend:

• #x → #y: #x needs to be completed before #y can be started
• #x | #y: #x or #y needs to be completed
• #x & #y: #x and #y needs to be completed