Installation

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

If you have an existing PYME installation, we recommend removing it before installing a new one.

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 create -n pyme python=3.6 pyme-depends-strict python-microscopy

To run programs from the command prompt, you will need to run conda activate pyme before running the program.

Note

The inclusion of pyme-depends-strict above pins all the PYME dependencies as well as their dependencies to fixed, known good versions. This blunt way of avoiding dependency conflicts was introduced after having been burnt once too often by packaging issues in our dependencies. It is particularly useful if you are also using uncurated channels such as conda-forge. In general omitting pyme-depends-strict, and simply running conda create -n pyme python=3.6 python-microscopy should be enough to give a functioning install, but there is a small chance that you will need to fix dependency conflicts.

Note

Which Python version? As of 2020/12/07, we recommend python 3.6 or 3.7 for new installs. We plan to add support for python=3.8 in the near future, but until such time downgrading to either 3.6 or 3.7 with and explicit python=3.x argument to conda create is required.

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.

PYMEVis

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.

Installation on python 2.7

On some instrument control computers, or when debugging potential regressions, it still makes sense to install PYME on python 2.7. We have stopped building packages on py2.7, so you’ll need a source install to get the most recent functionality and fixes. Unfortunately it is becoming increasingly difficult to conda install a consistent environment on python 2.7. As we are now focussed on py3 and things seem to change every couple of weeks we have given up on maintaining updated py 2.7 installation instructions. It is still possible to get things running, but it will be a bit of trial and error and you will need to manually up or downgrade some of the dependency packages. Good candidates for package conflicts would be traitsui, pyface, and wxpython. You might also need to use the full MS visual studio (community edition should suffice) rather than the stripped down msvc for python.

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.

Removing a PYME install

To remove an executable installer on Windows 10, go to Start Menu > Settings > Apps, find python-microscopy under Apps & Features, select it and press Uninstall.

To remove an executable installer on Mac, delete the python-microscopy folder, either in Finder or via the Terminal.

For conda installations on Windows, Mac and Linux, removing the conda envrionment (i.e. conda remove --name pyme --all, see the conda documentation for additional help) is the preferred method to delete PYME. If you want to completely remove any trace, you may also need to modify or remove .condarc and .bash_profile.