Getting started

Getting started

  • by orlandi

Prerequisites

  • MATLAB. The more recent the better. But any release after 2015 should work. Check the references page for a detailed list of (possibly) required toolboxes.
  • NETCAL should work on any modern OS (Windows, OS X and Linux).
  • If you want to correctly generate pdf/eps figures you’ll need ghostscript installed. If you use OS X or Linux you are probably good. On windows you can get it HERE
  • To be able to use any of the python modules you need python installed and available to MATLAB. If you have no idea how, you are probably running Windows, so just install something like Anaconda and point pyversion in MATLAB to the correct executable. Usually “pyversion(‘C:\Users\[YOURUSER]\Anaconda3\python.exe’)”

Download

You can download the latest release of the Open Beta HERE. Or check the releases section in Github.

Installation

  1. Unzip the downloaded file somewhere.
  2. Install additional MATLAB toolboxes: Go to the installDependencies folder and execute the mltbx files (or drag and drop in MATLAB).
  3. Change default MAT-Files version: Go to MATLAB Preferences -> General -> MAT-Files to v7.3
  4. To be able to export figures to pdf and eps you need ghostscript installed.

Running NETCAL

Within MATLAB, make the folder where you downloaded NETCAL your working directory and run: “netcal” on the command line.
NETCAL is structured around projects and experiments. Each project contains one or more experiments (usually several). An experiment is just a recording and its analysis. Note that no function within NETCAL (so far) will modify or write to the recording file.
In NETCAL you will spend most of your time in one of the three main modes. Easily identified by the tree big buttons on top of the main window:
  • Single experiment analysis This will be your bread and butter at the beginning. Within this mode you can use several GUIs on the View menu to interact with your recording. View the movie, the traces, etc. Any function that you run in this mode will only affect the selected experiment.
  • Batch mode In here you can run any analysis function on several experiments at once (on those with a checkmark). This mode also has several GUIs and statistical features that are only available when more than one experiment is selected.
  • Pipeline The best mode to work on large projects. In here you can create your own pipeline, i.e., a set of functions, to perform in sequence across all selected experiments. All functions present on the single experiment and batch mode also appear here (and many more). Note that the pipeline mode is designed for unsupervised use. So you will find very little GUIs in there.

Your first project

  1. To get started go to the File menu -> New Project. Create a new folder somewhere and name your project. It’s recomended to create a dedicated folder for each project. NETCAL will populate this folder with many files and folders.
  2. Now that you have created a project it’s time to add some experiments. You have three options to add new experiments:
    1.  Experiment menu -> Add from Movie/Stack. This is the standard option to add one recording at a time.
    2.  Experiment menu -> Add multiple movies. This option will recursively scan a chosen folder for new movies and let you select which ones to import.
    3.  Drag and drop. Just drag and drop any movie to the Experiment list panel and it should be added as a new experiment automatically.
  3. Now that you have added at least one experiment select it on the experiment list and it’s basic information and metadata should appear on the right. Make sure you are on single experiment mode!

Analyzing your first recording

  1. To be continued! (but essentially you do all the steps in the Analysis -> Fluorescence menu in order.