The second DAIS Learnathon took place from June 3 until June 9 2018.
This page is the Learnathon Wiki page of last year’s event!
Schedule
See this page!
Setting up your system
Check if you have this set up:
- Eclipse (Neon)
- bash / zsh
- GIT
- Maven
- Gitter
Monday
Intro session…
See slides!
Start a Maven project with Eclipse
See slides
Git repos to clone:
git@github.com:imagej/example-imagej-command.git
Notes: In case you want to switch to the legacy UI (ImageJ 1), you change the dependencies section in your POM to…
<dependencies>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej</artifactId>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-legacy</artifactId>
</dependency>
</dependencies>
Introduction to ImgLib2
Git repos to clone:
(Slides are contained in the repository.)
Tuesday
ImageJ2 and SciJava
- Search for stuff in our ecosystem: https://search.imagej.net
- SciJava and ImageJ Ops Jupyter notebook / slides
- Slides from last year’s Learnathon about SciJava community
- Developing ImageJ in Eclipse
ImageJ2 Ops
ImageJ Legacy
The ImageJ Legacy Course covered the topics: images, tables, regions of interest and command execution.
- ImageJ Legacy Exercises (Slides Included)
- Last years cheatsheet
- Last years course Slides Old Exercise 1 Old Exercise 2 Old Exercise 3
Jupyter Notebooks
- ImageJ2 Tutorial Notebooks
- Installation:
- Anaconda (we suggest miniconda) should be installed on your system.
- Clone to a place of your choice:
git clonehttps://github.com/imagej/tutorials - go into the tutorials folder you just cloned
- create a conda environment:
conda env create - activate the new environment:
source activate scijava - start jupyter notebook:
jupyter notebook
- Useful link to beakerx
- Python client for ImageJ
Git
- See the Git page!
Wednesday
KNIME Usage
- Download and install the KNIME Analytics Platform from here
KNIME Development Introduction
- Make sure you have Eclipse Oxygen installed
- Clone https://github.com/knime-ip/knip-sdk-setup
- Clone https://github.com/knime-ip/knip-course
Developing ImageJ Ops
- Clone https://github.com/imagej/tutorials (but you already have it, right?)
- Import
maven-projects/create-a-new-opin Eclipse. - See also the Adding new ops guide
- See also the “Extending ImageJ: Ops” notebook linked from here
ImageJ Server
- https://github.com/imagej/imagej-server
- imagej.server Python module
- Example Jupyter notebook using imagej-server
- Remote HPC cluster parallelization support in SciJava plugins
Thursday
ClearVolume and BDV VisTools
- Slides
- Repositories to be cloned:
- ImgLib2 Cache Examples (optional):
https://github.com/imglib/imglib2-cache-examples.git - Vistools live here:
https://github.com/bigdataviewer/bigdataviewer-vistools.git
scenery & sciview
- Slides / zipped keynote
- Repositories to be cloned:
- scenery repo:
https://github.com/scenerygraphics/scenery - sciview repo:
https://github.com/scenerygraphics/sciview
KNIME ImageJ2 Integration
- Course:
https://github.com/knime-ip/knip-course(Take a look at the README.md) - KNIP ImageJ2 repo:
https://github.com/knime-ip/knip-imagej2
Friday
Imglib2 Algorithm
- Slides: https://github.com/maarzt/imglib2-algorithm-workshop/blob/-/slides/presentation.pdf
- Exercises: https://github.com/maarzt/imglib2-algorithm-workshop
