Python scripts to run the OpenFlexure Microscope
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README.rst

openflexure_microscope_software

Python module to run the OpenFlexure Microscope

This repository contains the scripts that run the openflexure microscope. The bulk of the useful code is contained in the Python module openflexure_microscope, though there are some control scripts for characterisation experiments that currently live in a separate folder. These will be integrated into the main control program in due course.

Installation

Before you start

The microscope software can be installed using pip, which is now much simpler thanks to the absolutely brilliant PiWheels. If you are using the latest Raspbian image (October 2018) this should be set up for you already. If not, you just need to add a line to /etc/pip.conf (see the PiWheels web page for instructions). You will need a working internet connection for the commands below to work.

If you haven't previously used numpy or scipy you may need to install some numerical libraries. Open up a command prompt window and type:

sudo apt-get install libatlas-base-dev libjasper-dev

You will also need to set up the camera and, ideally, increase the GPU memory split to 256Mb, by running sudo raspi-config. You should first navigate to "interfacing options" and then "camera", and second you should choose "advanced options" and "memory split" to enter 256Mb. You will be asked to restart when you're done.

We recommend installing in a virtual environment, so that the microscope software doesn't interfere with your system Python distribution. You can do this with:

$ sudo apt install virtualenv python3-virtualenv -y
$ virtualenv -p /usr/bin/python3 microscope
$ source microscope/bin/activate

Whenever you want to use the microscope, you should first activate the environament by typing source microscope/bin/activate. You should see the command prompt change, showing you're using the virtual environment. When you are done, type deactivate to leave the virtual environment and switch back to using your system's Python installation.

Download and install

You should now switch to your virtual environment and download and install the microscope software (skip the source activate line if you are not using a virtual environment):

source microscope/bin/activate

wget https://github.com/rwb27/openflexure_nano_motor_controller/archive/master.zip
pip install master.zip
rm master.zip

wget https://github.com/rwb27/openflexure_microscope_software/archive/master.zip
pip install master.zip
rm master.zip

This will, by default, ensure you have the dependencies installed, including picamera. To use some features such as lens shading correction, you'll need to install my fork of picamera (at least until lens shading is incorporated upstream):

wget https://github.com/rwb27/picamera/archive/lens-shading.zip
pip install lens-shading.zip
rm lens-shading.zip

If your version of Raspbian is older than March 2018, you might not have the latest firmware - this is optional, but it allows you to to get full manual control of the camera (specifically to set gains and lens shading). You can update your firmware using sudo rpi-update stable if you have rpi-update installed, and sudo apt-get install rpi-update if not.

Once you have installed the module, you can run an interactive microscope control program by running the command openflexure_microscope in the terminal (see below). You can safely skip the installation of my forked picamera library, but you will get a warning and some features won't work. If you've not used your camera before, you may need to enable the camera module using sudo raspi-config and choosing "interfacing options" then "enable/disable camera". You will need to reboot afterwards.

Usage

If you are using a virtual environment as recommended above, you'll need to switch to that environment first, then run the microscope software:

source microscope/bin/activate
openflexure_microscope --help
openflexure_microscope

The module installs a command-line script, so you can run openflexure_microscope to start an interactive control program, or openflexure_microscope --help to see options. You can disable the motor controller by running openflexure_microscope --no_stage to run the software for the camera, without support for a motorised stage.

To recalibrate the microscope (which includes generating a new lens shading function), use openflexure_microscope --recalibrate. This requires you to first set the microscope up so that it is producing the most uniform image possible (i.e. the condenser lens must be properly aligned, and there must either be no sample present, or the sample must be well out of focus so it is not visible). The camera will start up and run for a few seconds, then the lens shading table will be adjusted to make the image uniform, and the camera will run for another few seconds - the image at this point should be uniform. Calibration settings (including lens shading and gain, etc.) will be saved to a file called microscope_settings.npz in the current directory, and this will be loaded by the interactive script the next time it is run.

Development

If you want to be able to modify the scripts, instead of installing with python setup.py install, use python setup.py develop. This leaves the scripts in the folder where they have been downloaded, but still links them into your system's Python path. That will allow you to run them as normal, but makes them easier to edit. Don't forget to commit your changes to Github - this may be easier if you first fork the repository on Github, then clone and install your copy of it. This is relatively simple: first, click the "fork" button at the top right of this repository's page - that will create a repository in your account. Next, go to that repository, and copy the URL from the "clone or download" link. It should look like https://github.com/<<your_username>>/openflexure_microscope_software.git where <<your_username>> is replaced with your username on GitHub. Then, replace my URL with yours, and run the same commands:

git clone https://github.com/<<your_username>>/openflexure_microscope_software.git
cd openflexure_microscope_software
python setup.py develop