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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.

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 development version of instamatic is available from here.

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

pip install -e .

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.

In order of priority:

1. Initialize the config directory

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

Go to the config directory from the first step.

In config/settings.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 (ranges/diff) and magnifications for your microscopes (ranges/lowmag and ranges/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 settings.yaml

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

It is recommended to run the temserver in a different terminal window by running instamatic.temserver if you specified this in settings.yaml. This helps maintain the microscope connection in case you want to restart instamatic. In some cases it is also worth to do this for the camera (or necessary in case of TVIPS) using instamatic.camserver.

Automatic config generation

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.

Installing the Gatan CCD plugin

To work with the gatan camera, instamatic needs a plugin for GMS. For this, instamatic depends on the RED CCD Plugin. You can download it here.

The plugin can be found in the package REDc.rar, in .\CCD_plugins\Gatan\Normal Gatan cameras\REDCCDPlugin.

Place REDCCDPlugin.dll in your Gatan plugin directory, which can usually be found here: C:\Program files\Gatan\DigitalMicrgraph\Plugins. For more information, have a look at the RED installation instructions manual.