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Laptop Computer Requirements
Students are required to bring a laptop in order to participate in the course hands-on tutorials. Laptop should be Windows or MacOS. Macbook Pro or Macbook Air, mid-2012 or newer model with 8GB memory and Mac OS 10.8.5 or later. For Windows laptops, Intel Core 2 or better processor, 8GB memory and Windows 7 Pro or later compatible OS. Your laptop should have a USB port as data files for the course will be distributed during class on a USB drive.
 
Students should make sure their laptop has 10GB of free disk space, a pdf viewer, and an up to date install of the Firefox, Chrome or Safari web browser. Administrator rights are required for installing some software packages we will use.
 
If you do not have access to a laptop meeting these specs we will do our best to accommodate you. To help us in planning, please email us the following specs for the laptop you will bring.
OS version:
Processor:
Memory:
Free Disk Space:
Web Browser Version:
PDF Viewer? Y/N
USB Port? Y/N
Administrator Rights? Y/N
MAC Address of your wireless network adapter: e.g. 36:c8:76:3d:2c:4d
_ _ _ _ _ _ _ _ _ _ _ _
Most of this information can be obtained by clicking on the "Apple > About This Mac" menu on Mac or from the "Control Panel > System" on Windows. The wireless MAC address is 12 characters with digits 0..9 and letters A..F. For instructions on locating your device's MAC address click here.
 
Preparing your laptop
If necessary, please update any system software on your laptop and make space on your hard drive by archiving old files. Also, it is always a good idea to backup your laptop before installing new software used for the course.
 
We recommend making a folder in your home directory or desktop called BigDIPA where you can store work on course materials and applications.
 
We will make use of the following software packages for course exercises and hands on experiments. The course will provide software licenses for use during the course for Globals and ViQi. We recommend you install Fiji, neuTube, Paraview and Anaconda prior to your arrival (see below for detailed instructions). We will also provide some time during the first day to help set up software.
 
Anaconda Python / Jupyter 3.5 (https://www.continuum.io/downloads)
Interactive scripting environment with libraries for image analysis, machine learning and general scientific computing.
 
Fiji is an image processing package, a "batteries-included" distribution of ImageJ bundling a lot of plugins which facilitate scientific image analysis.
 
neuTube is open source software for reconstructing neurons from fluorescence microscope images.
 
ParaView is an open-source, multi-platform data analysis and visualization application. ParaView users can quickly build visualizations to analyze their data interactively in 3D or programmatically and can be run on compute clusters to scale to very large datasets.
 
Fluorescence data analysis, simulation, and acquisition including tools for Fluorescence Correlation Spectroscopy (FCS)
 
A cloud platform for big image data management and analysis accessed through your web browser. A commercial version of the open source BisQue platform (http://bioimage.ucsb.edu/bisque)
 
Installing Python/Jupyter:
Exercises in machine learning and data analysis modules will be carried out using scripts written in Python. We will work with these scripts using Jupyter notebooks which are an easy way to interactively run the scripts and see the results in a web browser. We will utilize the Anaconda Python 3.5 distribution to make sure everyone has the same setup. You should install this on your laptop prior to the start of the course.
 

How to install Python/Jupyter on your machine:

  1. Download and install the Anaconda Scientific Python 3.5 64bit distribution. You can download the installer from here: https://www.continuum.io/downloads. The download will be ~400MB. Select the appropriate tab for your operating system. Make sure and choose the Python 3.5 version and 64 bit.
  2. You can find the installation instructions for each operating system here: https://docs.continuum.io/anaconda/install
  3. Once you have completed the installation, you should verify the installation and download any updates
  4. Verify the installation and update any Anaconda packages to the latest version.
    1. Open a terminal or command prompt (on Windows: Start - Command Prompt)
    2. To verify the install, enter the command “python” to run the Python shell. If Anaconda is installed and working, the version information it displays when it starts up will include “Continuum Analytics, Inc.” Type the command "quit()" to exit the Python shell.
    3. To update any Anaconda packages to their latest version, at the command prompt type “conda update conda” and press enter. Confirm that you'd like it to make any changes that it offers.
  5. Verify that you can run Jupyter notebook:
    1. Make a directory/folder called BigDIPA that you will use to store course materials
    2. Click https://bigdipa.bitbucket.io/install/test_notebook.ipynb.zip to download a demo notebook file, save it in the BigDIPA directory and unzip it.
      1. Start up Jupyter
      2. Open a terminal
      3. Change to the BigDIPA directory
      4. Type “jupyter notebook
      5. The interface to Jupyter will appear in your web browser. You should see the file you just downloaded visible.
      6. Click the file and a new tab will open, displaying a welcome message and a quick introduction to the Jupyter environment which you can work through.
  6. Click the "Cell" at the top of the opened notebook which contains the first bit of the test and then click "Run All"
    If you see error messages get in touch with us otherwise you should now be ready to carry out hands on exercises with Python!
Install Fiji
Fiji is a scientific image analysis package with a wide range of plugins. You can download Fiji from here: https://fiji.sc/. Make sure and select the 64bit version. The download is ~260MB. Once you download the the file for your operating system, you can unzip it into a folder in your BigDIPA directory. You do not need to “install” it in a particular location.
 
To run Fiji, navigate to the folder where you unpacked it and click on the executable. When Fiji runs, it will ask you if you want to start the Updater. Select “Yes, please. OK”. The update may take a few minutes to complete. Once it is done updating, it will display a message of success at which point you can close the updater window.
 
Install NeuTube
Download the latest version (1.0z.2016) here: http://www.neutracing.com/download/. The file is ~20MB. There is no special installation process. Double-click on the executable and see that it runs on your machine. Take a look at the tutorial videos here: http://www.neutracing.com/tutorial/ to get a feel for the software.
 
Install Paraview
Paraview is a visualization tool which allows for visualizing large complex datasets using a variety of methods. You can download from here: http://www.paraview.org/download/. Select version 5.2 ParaView Binary Installers and your operating system (Windows 64bit or MacOSX). The file will be ~300MB. While you are downloading you can check out the gallery of cool visualizations made with Paraview here: http://www.paraview.org/gallery/
 
Once you have downloaded and installed Paraview, run the application. You will see a window pop up which offers to show you some example visualizations. Take a few minutes to familiarize yourself with the tool.
 
You can find an extensive self-guided tutorial for Paraview here: http://www.paraview.org/Wiki/images/f/f7/ParaViewTutorial51.pdf
including datasets that go along with exercises in the tutorial http://www.paraview.org/Wiki/images/5/58/ParaViewTutorialData.zip
 
You do not need need to complete all the exercises but we recommend you look at Chapter 2.1-2.10 to get a basic grasp of the tool functionality.
 
Install SimFCS
For students with Windows laptops, we recommend you install the “Globals for Images · SimFCS 4” software, which we will use for visualizing and analyzing fluorescence microscopy data. For students with laptops running other OSes we will have a limited number of desktop machines on site where they will be able to use SimFCS.
 
The installer for the 64-bit version that will be used during the workshop is available at http://www.lfd.uci.edu/ftp/simfcs/simfcs4_workshop2016-setup.exe
 
Run the downloaded "simfcs4_workshop2016-setup.exe" installer. Administrator privileges are required.
 
On Windows 7 and 8.x, you may need to install the "Windows 10 Universal C Runtime", which is available at https://www.microsoft.com/en-us/download/details.aspx?id=48234. Many systems have it installed already.
 
Open the "SimFCS (64-bit)" shortcut in the "SimFCS 4_workshop2016" folder of the Windows start menu.
 
In case the "SimFCS Registration" program opens, enter your name and the license key we emailed to you. Administrator privileges are required. The license key will be valid until November 20.
 
There are a large set of tutorials at http://www.lfd.uci.edu/globals/tutorials/. We recommend you look at
Methods for 2-dimensional fluctuation analysis, e.g. Tutorial_2D_paircorrelationanalysis.pdf
 
 
Get Familiar with Python Scripting
If you are unfamiliar with Python, you should complete some online tutorials prior to the start of the course. We will have several hands-on lab tutorials which will make use of Python scripts so you will get much more out of the course if you come in with some basic understanding of the language.
 
Start with the “Learn the basics” chapters here: http://www.learnpython.org/ to make sure you understand the basics of the Python language itself.
 
We will use Python via Jupyter notebooks which provide a nice interactive way to run bits of Python code and see the results. We suggest the Jupyter “community documentation” available online here:
http://jupyter-notebook.readthedocs.io/en/latest/examples/Notebook/examples_index.html
 
In particular, the following three sections are quite useful.
If you would like to look further into using Python for scientific computation, here are two very useful online resources:
 
http://www.scipy-lectures.org/index.html : These online lecture notes provide a good introduction to Python as well as several standard libraries (NumPy, Matplotlib, Scipy) which are included in the Anaconda distribution and provide many useful functions for scientific computation and image processing.
 
https://docs.python.org/3.5/tutorial/ : A more in depth tour of the Python programming language.

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