color4/picasso

A collection of tools for painting super-resolution images

Picasso

A collection of tools for painting super-resolution images. The Picasso software is complemented by our Nature Protocols publication.

Installation

Check out the Picasso release page to download and run the latest compiled one-click installer for Windows. Here you will also find the Nature Protocols legacy version. For the platform-independent usage of Picasso (e.g., with Linux and Mac Os X) please follow the advanced installation instructions.

Advanced installation for Python programmers

As an alternative to the stand-alone program for end-users, Picasso can be installed as a Python package. This is the preferred option to use Picasso's internal routines in custom Python programs. For windows, one is still possible to use Picasso as an end-user by creating the respective shortcuts. This allows Picasso to be used on the same system by both programmers and end-users.

Requirements

Python 3.* (currently tested with 3.5)

We highly recommend the Anaconda or Miniconda Python distribution which comes with a powerful package manager.

Setting up environment with conda

Sample instructions to create an environment and installation of packages with conda are as follows:

1. Open the console and create a new conda environment: conda create --name picasso python=3.5
2. Activate the environment: source activate picasso for Linux / Mac Os X or activate picasso for Windows.
3. Install the necessary packages with conda: conda install h5py matplotlib numba numpy scipy pyqt=4 pyyaml scikit-learn colorama tqdm
4. Additionally install the lmfit package with pip: pip install lmfit
5. (Optional) If you plan to compile your own installer additionally install Pyinstaller: pip install pyinstaller
6. Continue with the installation of Picasso

Note that sometimes outdated packages can cause problems. If you experience errors, please check whether your packages have the right version (e.g. see issue #4). Also note that there is also a requirements.txt which you can use to install all packages with pip (pip install -r requirements.txt). However currently you will also need PyQt4 (i.e. with conda install pyqt=4 -y). In the past, not relying on conda caused troubles with creating the one-click installer. I therefore recommend installing all packages with conda.

Installation

1. Open the console, cd to the directory where you want to install and run git clone https://github.com/jungmannlab/picasso Alternatively, download the zip file and unzip it.
2. Change to the downloaded directory cd picasso
3. Run installation python setup.py install.

Optional for windows users

Run the PowerShell script "createShortcuts.ps1" in the gui directory. This should be doable by right-clicking on the script and choosing "Run with PowerShell". Alternatively, run the command powershell ./createShortcuts.ps1 in the command line. Use the generated shortcuts in the top level directory to start GUI components. Users can drag these shortcuts to their Desktop, Start Menu or Task Bar.

Using Picasso as a module

The individual modules of picasso can be started as follows:

1. Open the console, activate the enviroment: source activate picasso for Linux / Mac Os X or activate picasso for Windows.
2. Start the picasso modules via python -m picasso .., e.g. python -m picasso render for the render module

Using GPU for Fitting

To enable GPU fitting, follow instructions on Gpufit to install the Gpufit python library in your conda environment. Picasso Localize will automatically import the library if present and enables a checkbox for GPU fitting when selecting the LQ-Method.

Contributions & Copyright

Contributors: Joerg Schnitzbauer, Maximilian Strauss
Copyright (c) 2015-2018 Jungmann Lab, Max Planck Institute of Biochemistry

Credits

• Design icon based on "Hexagon by Creative Stalls from the Noun Project"
• Simulate icon based on "Microchip by Futishia from the Nount Project"
• Localize icon based on "Mountains by MONTANA RUCOBO from the Noun Project"
• Filter icon based on "Funnel by José Campos from the Noun Project"
• Render icon based on "Paint Palette by Vectors Market from the Noun Project"
• Average icon based on "Layers by Creative Stall from the Noun Project"