Welcome, this is the repository to contain the original branch of the mtFociCounter.
In this repository you will find:
A) several scripts which can be run and convert data.
B) several text-files on different topics.
In this read-me, we will first list all the files with a short explanation on what they are and contain:
i) a jupyter notebook (file-ending ipynb): 20211208_CytbKO_foci.ipynb
This is an old version of a jupyter notebook which could serve as a template to analyse the data output by the Fiji-plugin "Foci Counter"
Do not worry too much about it, it will be replaced in the future with something more robust and simpler to use - hopefully as a python-based web-application
ii) a jython-file called: FociCounter_b10_.ijm
This is the current version with minor upgrades from the previous beta versions for better usability.
Please have a go and report anything that you are not happy with via e-mail to me! [firstname + lastname, as indicated within the script, at hotmail.com]
NOTE: further updates may be added in the future.
i) This README.md
This mainly servers as a center for orientation and should be updated every now and then.
ii) A UserGuide.md
This gives a basic explanation of how to use the mtFociCounter.
It contains a step-by-step guide to how to install and run the plugin, and explains briefly what choices are available and what they are good for.
iii) Code-logic This does not yet exist, but should later allow to understand the logic of the script, what algorithms are used, and how the different sections work.
iv) Future directions:
This does not yet exist but will contain my planned updates and ideas for future features.
You are welcome to add your own branches with ideas!
v) Developer instructions:
This does not exist yet, but I hope to eventually write this file to help guide potential efforts to improve the code to where I believe they would be best invested.