search

NEUBIAS / training-resources

Resources for teaching/preparing to teach bioimage analysis
https://neubias.github.io/training-resources
Other
45 stars 21 forks source link

Scripting: Module how to set up the environment #165

Open tischi opened 2 years ago

tischi commented 2 years ago

Maybe a good idea to also add a module for how to set up the environment?

Fiji Macro:

Napari:

@stemarcotti @manerotoni

manerotoni commented 2 years ago

Hi @tischi, in this setup session we can also add what we normally ask users to do for the basics course (always in documentation at beginning of course):

For the start-up macro: Edit > Options > Startup ... Add Code > Black Background

tischi commented 2 years ago

Install Fiji

Done

Enable update site IJBP-plugins

Done

Make in settings for black binary background. This is not remembered anymore.

I don't think this is best practice, because your macro will not run properly on some else computer. I am afraid on has to add it to each macro (boilerplate). I think we can discuss this in the Running a script module. OK?

Test some features using sample images (test drag&drop)

You mean from the training website? Maybe we need an even more general module about "setting up your image analysis platform" (without scripting)?

git download the images

Usually we don't need this, because we load from the website...

tischi commented 2 years ago

I made a brunch script_env to work on this. I already merged a draft: https://neubias.github.io/training-resources/script_env/index.html

manerotoni commented 2 years ago

I don't think this is best practice, because your macro will not run properly on some else computer. I am afraid on has to add it to each macro (boilerplate). I think we can discuss this in the Running a script module. OK?

Hi @tischi, Yes we do need to add it to every script :-(

However, I think it is useful to explain general settings. This is normally how you would work on your computer. You set up the environment once and then you go.

When we teach, we explain how to use the material, what to download and install. We can have a module (I think you created some suggestions) that explains how to setup things. Honestly, I am not sure if it should be a module. We are not teaching a general principle and I would not clutter the teaching material with techinical details. Why not a plain markdown part? We could refer to it from the main page. The advantage of the plain markdown is that we could easily modify it as we go along.