The tutorials consist of lecture segments, demos, and hands-on exercises. We strongly encourage you to bring a laptop with all the required packages installed in order to participate fully.
Some of the tutorials will be using a data-set of cell images kindly provided by Maryana Alegro (UCSF). The data is available to download here.
The Azure tutorial will use an image data-set described in this webpage. Please use the link on the page to download the data.
If you are new to Python, please install the Anaconda distribution for Python version 3 (available on OSX, Linux and Windows). Or, feel free to use your favorite distribution, but please ensure the requirements below are met:
In Anaconda, install these packages with:
conda install numpy scipy matplotlib jupyter scikit-image scikit-learn dask pip install conda tensorflow # or tensorflow-gpu if you have an Nvidia graphics card
In any other Python distribution, use pip:
pip install numpy scipy matplotlib jupyter scikit-image scikit-learn dask keras tensorflow # or tensorflow-gpu if you have an Nvidia graphics card
In the next section below, we provide a test script to confirm the version numbers on your system.
Please run this test script to verify your package versions.
E.g., on my computer, I see:
$ python check_setup.py [✓] numpy 1.12.1 [✓] scipy 0.19.0 [✓] matplotlib 2.0.0 [✓] notebook 4.3.1 [✓] scikit-image 0.13dev [✓] scikit-learn 0.18.1 [✓] dask 0.14.0 [✓] tensorflow 1.0.0 Using Theano backend. [✓] keras 2.0.2
To update a package, use:
conda upgrade package_name # for conda pip install --upgrade package_name # for pip
If you do not have a working setup, please contact the instructors.
Installation instructions are available here
For this demo we will use samples that will be fetched from the imagej.net site through the application, so no separate downloads are required.
We encourage downloading Beaker and opening the ImageJ tutorials notebook prior to the tutorial. This will automatically fetch the necessary dependencies.
Recently the ImageJ community has begun using Beaker Notebook for interactive coding. Beaker is like Jupyter notebook, but is built upon the JVM. It has some unique features that are a bit more challenging to incorporate into Jupyter notebook; in particular, Beaker is a polyglot notebook where switching between languages within a single notebook while maintaining access to the same scope/variables.
Beaker installation instructions are available here (only the “base install” is required).
There are two ways of downloading the lecture materials:
a) Get the ZIP file from GitHub
b) Clone the repository at https://github.com/imagexd/2017-tutorials
We will work through the ImageJ beaker tutorial from the imagej-tutorials github repository, which can either be checked out from the repository: https://github.com/imagej/tutorials
Or downloaded directly with this link
In this tutorial, we will build an SVM based image classifier using Azure Machine Learning. You will learn how to use Azure storage, get familiar with the Azure portal, and with Azure Machine Learning. Participants will be given $500 worth of Azure credits that will be valid for one month
Please download the latest version of the material on the morning of the tutorials to be sure you have all updates.