diff --git a/README.md b/README.md index 18b552bf941a68b66daef07bcf80521093a5eb99..0ed7c5ba0862a6088f6ad3fff681467e51bcb20f 100644 --- a/README.md +++ b/README.md @@ -18,7 +18,7 @@ - Guided walk-through - Exercises -Slides available [here](). +Good slides available [here](https://docs.google.com/presentation/d/1u_FraZPABjCdzNj_2Oq5i7FxWbGPdIkbtCKXzxAORwA/edit?usp=sharing). ## This repository @@ -33,7 +33,7 @@ Follow the instructions provided [here](https://iah-public.pages.pasteur.fr/bioi ### Alternative: Run the notebooks in the cloud -The notebooks in this repository can be run interactively using different cloud services. You can use the badges at the top of this Readme to run the notebooks either +The notebooks in this repository can be run interactively using different cloud services. You can use the badges at the top of this README to run the notebooks either - in the classical Jupyter environment via - MyBinder - Renkulab (with graphical support to run `napari`) diff --git a/_config.yml b/_config.yml index 0530ad5ddfc8e7d7c63c9231cfa6aaf043bb9daf..0274e5bc14cdf9cf536b025d1f14f03df1bbebe5 100644 --- a/_config.yml +++ b/_config.yml @@ -1,6 +1,6 @@ # Book settings -title: "Course: Image processing with Python for beginners" +title: "Course: BioImage processing with Python for beginners" author: Guillaume Witz -#logo: 'logo.png' +# logo: 'logo.png' execute: execute_notebooks: "off" \ No newline at end of file diff --git a/_toc.yml b/_toc.yml index 863a78a76f6b552f4785a680e0c5745f8d68be1e..12750e866809cfdd7d5709991400b8c13ba0a736 100644 --- a/_toc.yml +++ b/_toc.yml @@ -1,19 +1,21 @@ format: jb-book root: README chapters: +- file: book/install_python.md - file: book/download_repo.md - file: book/setup_environment.md - file: book/launch_notebooks.md -- file: 01-Python_essentials -- file: 02-Images_as_arrays -- file: 03-More_on_images -- file: 04-Thresholding -- file: 05-Filtering -- file: 06-Regions -- file: 07-Pipeline -- file: 08-Logical_flow -- file: 09-Advanced -- file: Appendix_Functions -- file: Appendix_Structures -- file: Cheatsheet -- file: Demo \ No newline at end of file + sections: + - file: notebooks/01-Python_essentials + - file: notebooks/02-Images_as_arrays + - file: notebooks/03-More_on_images + - file: notebooks/04-Thresholding + - file: notebooks/05-Filtering + - file: notebooks/06-Regions + - file: notebooks/07-Pipeline + - file: notebooks/08-Logical_flow + - file: notebooks/09-Advanced + - file: notebooks/Appendix_Functions + - file: notebooks/Appendix_Structures + - file: notebooks/Cheatsheet + - file: notebooks/Demo \ No newline at end of file diff --git a/book/download_repo.md b/book/download_repo.md index 460d928ece8455bc90c00801c96c4251e1c1a11e..45e2e402b0de3bcccbec83fa89a5e632fcb286c8 100644 --- a/book/download_repo.md +++ b/book/download_repo.md @@ -1,6 +1,6 @@ # Downloading the course material -## Downloading the notebooks. +## Downloading the notebooks During this tutorial, we will be working through a set of notebooks. On this page, we will download the notebooks and launch jupyter notebook. There are two ways to download the notebooks: download as a .zip from github. Follow the instructions below for either "downloading zip" (recommended for beginners) or "cloning via git". ### Downloading .zip diff --git a/book/install_python.md b/book/install_python.md index a430a6bcbe51855250d8248bea1609a7ee684fa1..b4900c4e46fd2b3dda7aad96b3d294474ee066c5 100644 --- a/book/install_python.md +++ b/book/install_python.md @@ -1,7 +1,14 @@ -# Install python +# Installing Python ## Overview -This how-to teaches how to install python on your computer using `mambaforge`. `mambaforge` is a python distribution pre-installed with the [`mamba`package manager](https://mamba.readthedocs.io/en/latest/index.html) and pre-configured to use the `conda-forge` channel. I generally recommend installing this route, as I find it to be the most straight forward and I prefer to use `mamba` over `conda`, as it is much faster. +This how-to teaches how to install Python on your computer using `conda`, which is both a + +- environment manager and a +- package manager. + +### `conda` and `mamba` + +There is one problem with conda: Its default package manager is very slow. Instead, using `conda` in combination with the package manager [`mamba` package manager](https://mamba.readthedocs.io/en/latest/index.html) saves a lot of time when installing new packages. The version of `conda` which includes this package manager is called `mambaforge`. **Prerequisites** - You have a computer with linux, MacOS, or Windows installed @@ -16,7 +23,7 @@ Select the installation instructions for your operating system and processor fro ````{tab-set} ```{tab-item} Linux -1. In your web browser, navigate to the [miniforge page](https://github.com/conda-forge/miniforge#mambaforge). +1. In your web browser, navigate to this [download page](https://github.com/conda-forge/miniforge#mambaforge). 2. Scroll down to the "Mambaforge" header of the "Downloads" section. Click the link to download link for `Mambaforge-Linux-x86_64`. 3. Open your terminal application 4. Navigate to the folder you downloaded the installer to (usually this is in your Downloads folder). If the file was downloaded to your Downloads folder, you would enter: diff --git a/book/launch_notebooks.md b/book/launch_notebooks.md index 0780eb3a0bf57e893b15cc4b53e3576de01e4b09..c60af9cf3fcce71e719b6a30eadef58a2d06d591 100644 --- a/book/launch_notebooks.md +++ b/book/launch_notebooks.md @@ -2,10 +2,10 @@ ## Launch jupyter notebook -Open your terminal and navigate to the `bioimage_analysis_with_python_course` directory you downloaded. +Open your terminal and navigate to the `notebooks` subdirectory of the `bioimage_analysis_with_python_course` directory you downloaded. ``` -cd <path to bioimage_analysis_with_python_course> +cd <path to bioimage_analysis_with_python_course>/notebooks ``` Now activate your `pyimagecourse` conda environment you created in the installation step. @@ -20,4 +20,19 @@ To start the Jupyter Notebook server, enter jupyter notebook ``` -Jupyter Notebook will open in a browser window and you will see the course notebooks. \ No newline at end of file +Jupyter Notebook will open in a browser window and you will see the course notebooks. + + +### Alternative: Run the notebooks in the cloud + +The notebooks in this repository can be run interactively using different cloud services. You can use the badges below to run the notebooks either +- in the classical Jupyter environment via + - MyBinder + - RenkuLab (with graphical support to run `napari`) +- as Google Colab notebooks + +The Mybinder and Renkulab sessions are only temporary, i.e. changes you make to notebooks or new notebooks are *erased* between sessions. When using Colab, to keep your changes, you need to *save a copy* of the notebook you are modifying. The saving is done in your Google Drive. + +[](https://mybinder.org/v2/gh/m-albert/PyImageCourse_beginner/master?urlpath=lab) +[](https://colab.research.google.com/github/m-albert/PyImageCourse_beginner/blob/master) +[](https://renkulab.io/projects/marvin.albert/pyimagecourse-beginner/sessions/new?autostart=1) \ No newline at end of file diff --git a/book/setup_environment.md b/book/setup_environment.md index 1b5c885b320c567502054beb3e060553fb57d996..fda6b322e4f8574409e3291540231bffb26af1af 100644 --- a/book/setup_environment.md +++ b/book/setup_environment.md @@ -44,7 +44,7 @@ To install python via mambaforge, follow the instructions [here](install_python. ## Setting up your environment ```{admonition} Using conda instead of mamba? -The following assumes that you have installed python using Mambaforge as [described above](content:references:napari_python_installation). If you are using a pre-existing installation of python via anaconda, miniconda, or miniforge, consider installing `mamba` into your existing installation using the command `conda install -c conda-forge mamba`. Alternatively, you can simply replace the `mamba` commands below with `conda`. +The following assumes that you have installed python using Mambaforge as [described above](install_python.md). If you are using a pre-existing installation of python via anaconda, miniconda, or miniforge, consider installing `mamba` into your existing installation using the command `conda install -c conda-forge mamba`. Alternatively, you can simply replace the `mamba` commands below with `conda`. ``` diff --git a/environment.yml b/environment.yml index f56a401f08af807998827ec59357eeeb5d5e9c4d..ea11d0afd7c9ef5d909577bc4febbcbd90abd975 100644 --- a/environment.yml +++ b/environment.yml @@ -2,6 +2,7 @@ name: pyimagecourse channels: - conda-forge dependencies: + - python=3.10 - napari - pip - pip: diff --git a/01-Python_essentials.ipynb b/notebooks/01-Python_essentials.ipynb similarity index 100% rename from 01-Python_essentials.ipynb rename to notebooks/01-Python_essentials.ipynb diff --git a/02-Images_as_arrays.ipynb b/notebooks/02-Images_as_arrays.ipynb similarity index 100% rename from 02-Images_as_arrays.ipynb rename to notebooks/02-Images_as_arrays.ipynb diff --git a/03-More_on_images.ipynb b/notebooks/03-More_on_images.ipynb similarity index 100% rename from 03-More_on_images.ipynb rename to notebooks/03-More_on_images.ipynb diff --git a/04-Thresholding.ipynb b/notebooks/04-Thresholding.ipynb 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