Installation

The best to install PYME will depend on your background and whether you are already using python on your computer.

Executable installers (Windows and OSX)

Recommended if you don’t already have python on your computer and/or are unfamiliar with python. Download the latest installer from https://python-microscopy.org/downloads/. Double-click the installer and follow instructions.

Installing using conda

Download and install Miniconda. Then, open the Anaconda prompt 1 and enter

conda config --append channels anaconda
conda config --add channels david_baddeley
conda install python-microscopy

Note

Which Python version? We are in the process of switching the default install from Python 2.7 to Python 3.6. As of 2020/09/25, we support python 2.7, 3.6 & 3.7. The Python 2 version is currently better tested, but most of the core functionality runs on Python 3. Due to ongoing changes in the anaconda repositories, installation on Python 3 tends to be easier. We aim to drop Python 2 support in January of 2021.

Updating

Assuming that you’ve installed using either the executable or conda routes, you can update PYME by dropping into the Anaconda prompt 1 and entering:

conda update python-microscopy

Development installs

This assumes a basic familiarity with python and conda. We maintain a conda metapackage, pyme-depends for PYMEs dependencies, and reccomend a separate conda environment for development installs. Entering the following at the command prompt should get you a functional system, alter to suit your needs:

conda config --add channels david_baddeley
conda create -n pyme pyme-depends python=X.X
conda activate pyme

git clone https://github.com/python-microscopy/python-microscopy.git
cd python-microscopy
python setup.py develop

On OSX, use /path/to/conda/environment/python.app/Contents/MacOS/python setup.py develop instead of python setup.py develop so that the PYME programs can access the screen.

Enable bioformats data importers

Install a JAVA JDK or JRE. Open a command prompt in the installation conda environment and enter

conda install javabridge
conda install python-bioformats

Caveat: This currently only works on OSX. If conda packages for javabridge and bioformats don’t work, try pip.

Verify installation

Locate the PYMEVisualize (VisGUI) desktop shortcut. Double-click it and confirm the program launches. If you don’t have a desktop shortcut, launch any of the following programs from an anaconda prompt, which should have been installed as part of PYME.

PYMEImage -t

This is for viewing images. The -t option initiates a test mode which displays an image of random noise.

PYMEAcquire

This for acquiring data from a custom microscope. When launched without any options, it will start with simulated hardware. It will display a live image of random noise, streamed from a simulated camera.

PYMEVisualize

This is for viewing point data sets. It shows a blank canvas when launched without any parameters.

Troubleshooting

Executable installers

If prompted with Windows protected your PC, click More info and then Run anyway.

If prompted with Installation error, press OK and then Ignore.

Developer installs [OSX]

On OSX, the following error may appear when launching a PYME application from the command line.

This program needs access to the screen. Please run with a Framework build of python,
and only when you are logged in on the main display of your Mac.

This can be solved by the following.

cd /path/to/python-microscopy/
/path/to/mininconda/install/python.app/Contents/MacOS/python setup.py develop

Additional resources

pip installation [EXPERIMENTAL]

You can also install PYME using pip, although we recommend this as a last resort as a conda based installation will generally give better performance and should be easier. When using pip, you might need to manually hunt down some dependencies, and for dependencies which don’t have binary wheels, you might need to spend a lot of time setting up the development evironment and finding the DLLs etc which dependencies link against. Some of our dependencies also need to be compiled using gcc (rather than MSVCC), even on windows. Because we view this as a fallback when, e.g. conda can’t come up with a resolvable set of dependencies, or when you are installing on top of a bunch of existing packages, the pip packages depend only on numpy, with the rest of the dependencies being installed separately through the use of a requirements.txt file.

pip install -r https://raw.githubusercontent.com/python-microscopy/python-microscopy/master/requirements.txt
pip install python-microscopy

If installing in a tricky evironment, you can manually edit requirements.txt before installing. You can also use the top line to setup for a development install.

Footnotes

1(1,2)

On OSX or linux this is the command prompt. On Windows, this is accessed from the “Miniconda” or “PYME” folder in the start menu.