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Setting up Instamatic

Download the latest zip package from the releases page. This installation is fully portable, and can be copied directly to the microscope computer.

Running the program start_Cmder will run a terminal which has already been set up.

JEOL

If you are using a JEOL TEM, make sure instamatic is installed on a computer with the TEMCOM interface. This is usually already installed on the camera PC. It can also be installed on the microscope control PC.

FEI

For FEI microscopes, instamatic must be installed on the microscope control PC. Alternatively, it can be installed on both the microscope PC and the camera PC, running instamatic.temserver on the microscope PC, and establishing a connection over the local network. See the config documentation for how to set this up.

Development version

The latest, bleeding edge development version of instamatic is available from here.

If you run the portable installation, just extract and replace the instamatic directory in the root directory of the installation (the one that contains start_Cmder.exe). Make sure to delete the old one before.

If you want to install instamatic into your own python installation, just extract and run:

pip install -r requirements.txt
python setup.py install

Setting up the config files

Normally instamatic is not very fussy about starting up, but it may complain if you try to run some commands where it is missing some information from the config.

The easiest way to get started is to run:

instamatic.autoconfig.exe

To help generate some of the input files (in particular templates for the microscope/calibration files). This should give you a working setup for the microscope.

In order of importance:

  1. Initialize the config directory
    If you are running the portable installation, you can skip this step. Otherwise, if you are running instamatic for the first time, it will set up the config directory. Simply run instamatic. It should say that it sets up the config directory and tell the path where the data are.

  2. Set up the microscope interface
    In config/global.yaml define the camera interface you want to use. You can use the autoconfig tool or one of the example files and modify those. You can name these files anything you want, as long as the name under microscope matches the filename in config/microscope

  3. Set up the magnifications and camera lengths
    In the config file, i.e config/microscope/jeol.yaml, set the correct camera lengths (range_diff) and magnifications for your microscopes (range_lowmag and range_mag1). Also make sure you set the wavelength. Again, the autoconfig tool is your best friend, otherwise, the way to get those numbers is to simply write them down as you turn the magnification knob on the microcope.

  4. Set up the camera interface
    Specify the file you want to use for the camera interface, i.e. camera: timepix points to config/camera/timepix.yaml. In this file, make sure that the interface is set to your camera type and update the numbers as specified in the config documentation. If you do not want to set up the camera interface at this moment, you can use camera: simulate to fake the camera connection.

  5. Make the calibration table
    For each of the magnfications defined in config/microscope/jeol.yaml, specify the pixel sizes in the file defined by calibration: jeol, corresponding to the file calibration/jeol.yaml. For starters, you can simply set the calibration values to 1.0.

  6. Test if it works
    Run instamatic.temcontroller to start a IPython shell that initializes the connection. It should run with no crashes or warnings.

  7. Update global.yaml
    There are a few more choices to make in instamatic/global.yaml. If you use a TVIPS camera, make sure you put use_cam_server: true.

It is often a good idea to run the camserver and temserver in a different terminal window by running instamatic.temserver / instamatic.camserver if you specified this in global.yaml.

Other directories

  • cmder: Contains the Cmder software package. The file cmder\config\user-profile.ps1 can be used to set up the environment variables, and extra programs can go into cmder\bin.
  • config: Contains all the config files for instamatic
  • instamatic: Source code for instamatic. Replace this directory if you want to update instamatic.
  • logs: Log files from instamatic are stored here.
  • python36: This contains the portable python installation and libraries
  • scripts: The instamatic GUI picks up scripts from this directory.