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Setup

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kaczmarek-kamil edited this page Jan 26, 2018 · 20 revisions

Setup

There are two main ways to start working with this workshop.

(recommended) Option 1: Google Colaboratory

According to the project's main page:

Colaboratory is a Google research project created to help disseminate machine learning education and research

It is free to use for education and research purposes and we will use it in our workshop. It enables us to work interactively with the Python code directly in your browser.

Setup

step 1: download the repository to disk

  1. open terminal
  2. cd to your working directory
  3. copy workshop contents to your disk:
$ git clone https://github.com/WUT-ML/appliedmldays_2018.git

Alternatively you can just go to the workshop page on GitHub and click clone or download to download entire repository.

step 2: setup Google Colaboratory

  1. Log in to your Google account
  2. Go to: Google Colaboratory
  3. Upload workshop notebook

step 3: download data

Zebrafish imaging data is available for download here: dataset.

At this point you are all set.

😃

Option 2: local setup

This option is targeted towards users who are comfortable with command line, git, and source code handling. We support only Ubuntu machines. If you are on other OS, we will try to figure out best solution for you.

step 1: download the repository to disk

  1. open terminal
  2. cd to your working directory
  3. copy workshop contents to your disk:
$ git clone https://github.com/WUT-ML/appliedmldays_2018.git

step 2: setup local environment

  1. create virtualenv:
$ virtualenv workshop -p python3.5
  1. activate virtualenv:
$ source workshop/bin/activate
  1. install required packages:
$ pip3 install -r requirements.txt
  1. start Jupyter notebook
$ jupyter nbextension enable --py widgetsnbextension
$ jupyter notebook

note that in case of issues try this command: jupyter nbextension enable --py widgetsnbextension --sys-prefix and then jupyter notebook.

step 3: download data

Zebrafish imaging data is available for download here: dataset.

Other remarks

Advanced Users may want to Install Fiji: image processing package implemented in Java. Fiji is a tool that will let you easily browse raw data.

At this point you are all set.

😃

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