CBIAS napari workshop 2024 - run as part of the Crick Bioimage Analysis Symposium 2024
27-28 November 2024
The Francis Crick Institute
https://www.crick.ac.uk/whats-on/cbias-napari-workshop-2024
This training is developed and delivered by Rocco D’Antuono (the Francis Crick Institute), Giulia Paci (University College London) and Marie Held (the University of Liverpool). Additional speakers include Ana Stojiljkovic (University of Bern), Sebastian Gonzalez Tirado (Heidelberg University), Cameron Shand (the Francis Crick Institute) and Graham Ross (the Francis Crick Institute).
We are kindly helped in the organization of the workshop by the Crick External Training team, Lorenza Giannella and Erdal Dogan.
This training provides fee waivers offered thank to the support of the Chan Zuckerberg Initiative
During the workshop we will extensively try and retry the software installation with conda environments, however to gain some practice and proceed smoothly to more interesting topics, please proceed with the following homework before the workshop
- Install Anaconda Navigator
- Install napari within conda prompt
Please make sure to have at least 10-15 GB free on the pc you will bring with you for participating in the workshop. Please let us know well in advance if you cannot bring a pc with you, we might be able to get a loan, however this is not guaranteed and you might risk to have no pc to follow along.
This is a method that use the graphical user interface to download and install Anaconda Navigator. Please visit https://docs.anaconda.com/ and click on the green button "Download Anaconda". You will be asked to provide an email address and will receive the link to the download page, where you will choose the version for your OS.
Before installing Anaconda Navigator, please identify a folder in your computer over which you have full permission of read and write file: we will create and update many times conda environments, this means that the software will install and remove files all the times.
The successful installation of Anaconda Navigator will make available an app called "Anaconda prompt". Thsi is the terminal that we will use to create and work with conda environments.
a) Update conda, by typing the following line and pressing Enter.
conda update -n base -c conda-forge conda
b) create a new environment with a meaningful name: substitute with your choice the string "mymeaningfulname". E.g. "cbias-workshop-env". Please do not simplify with "napari-env", as half of the tutorial use that and you might risk to overwrite a previous environment which contain packages used in previous analyses.
conda create -n mymeaningfulname-env python=3.12
c) activate the new environment
conda activate mymeaningfulname-env
You should notice a change in the prompt where the name base at the beginning of the prompt has been changed to "mymeaningfulname-env". This confirms that it is safe to install new packages, as you are not altering the base environment (safe choice is not touch "base").
d) install napari
conda install -c conda-forge napari pyqt
e) check that napari opens At this point, if no error appears in the terminal as result of the operations above, you are ready to open napari executing
napari
If a working environment cannot be created through the commands above, the following recipe can be used to create an environment with napari
a) Download the file cbias2024-napari-env.yml into a local folder
b) use the Anaconda prompt to navigate to the local folder and execute
conda env create -f cbias2024-napari-env.yml
This should create an environment with the same name of the .yml file unless otherwise specified.
c) check that napari opens At this point, if no error appears in the terminal as result of the operations above, you are ready to open napari executing
napari
Install napari with options 1 and 2 above or the provided recipe (.yml file).
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Basic 3D image segmentation with napari-zelda (Rocco D’Antuono) Follow Option D in the napari-zelda plugin repository or download this cbias2024-napari-zelda-env.yml file, use the Anaconda prompt to navigate to the local folder and execute
conda env create -f cbias2024-napari-zelda-env.yml -
EpiTools: a napari plugin for quantifying epithelial dynamics (Giulia Paci) For installation instruction visit Epitools repository
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Mitochondria segmentation in EM data with napari-empanada (Marie Held) Either execute the following (note the python version must not be >3.9!)
conda create -n empanada-ws-env python=3.9 conda activate empanada-ws-env conda install -c conda-forge napari pyqt pip install empanada-napariAlternatively, download the cbias2024-napari-empanada-env.yml file, use the Anaconda prompt to navigate to the local folder and execute
conda env create -f cbias2024-napari-empanada-env.yml -
Interactive pixel classification using pretrained neural networks with napari-convpaint (Ana Stojiljkovic)
Once you have installed napari in your environment using Option 1 or 2 above, you can install the napari convpaint plugin from PYPI:pip install napari-convpaint -
Easy movie creation with napari-animation (Ana Stojiljkovic)
To easely create movies to document your image analysis results (.mp4, .gif, .mov, .mkv), add the napari-animation plugin to your napari environement. We recommend installing it from conda-forge, especially if you are using macOS. For detailed installation instructions, visit the napari-animation repository.conda install -c conda-forge napari-animationIf you prefer please use the cbias24-napari-convpaint.yml file to install a napari environment containing both plugins, napari-convpaint & napari-animation.
Slides for the napari-convpaint & napari-animation showcase.
- Introduction to Jupyter notebooks for bioimage analisis with python (Rocco D’Antuono) Create and environment with Jupyter lab to execute python notebooks, with the following commands
conda create -n cbias2024-jupyter-env python=3.10
conda activate cbias2024-jupyter-env
conda install jupyterlab
conda install -c conda-forge napari pyqt
conda install matplotlib
or re-create the environment downloading this cbias2024-jupyter-env.yml file and executing the following commands in Anaconda prompt (need to be in the local folder where the file is):
conda env create -f cbias2024-jupyter-env.yml
- Delving into Napari layer types (Sebastian Gonzalez Tirado)
- Napari widgets and plugin creation with magicgui and plugin template (Cameron Shand) Instruction on the plugin creation demo: https://github.com/FrancisCrickInstitute/cbias2024_napari_demo
- Introduction to image registration methods for 2D and 3D image data (Graham Ross)
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