Getting Started

In order to be able to control stage positions (which are used for focus and sample positioning), toggle lasers, trigger cameras, and so on, you first need to set up a connection to your hardware. This guide will walk you through the steps necessary to get your system up and running.

Hardware Setup

Unlike other microscopy systems, Altair simplifies control by having only one controller - one apparatus to trigger and drive all necessary devices. This is Applied Scientific Instrumentation’s Tiger Controller, a modular controller with customizable control cards. Our solution calls for a tiger controller with the following cards:

  • TGCOM - allows Joystick control and serial communication from computer

  • 3 Stage control cards - (X/Y, Z/F, M/N)

  • 2 DAC4 cards - Analog signal generators

  • TGPLC - Programmable Logic Controller which provides for custom timing

  • FW-1000 - Filter Wheel Control

The order of these cards within the controller does not matter. The software to run the controller is navigate. Navigate supports many microscope configurations, where each configuration is defined by a configuration file. The provided configuration file will delineate the following configuration:

Axis

Device

A

Remote Focus Voice Coil

B

Galvanometer

H

405 nm Laser (Analog)

I

488 nm Laser (Analog)

J

561 nm Laser (Analog)

K

638 nm Laser (Analog)

1

Camera Trigger

2

Laser Shutter

3

Stage In

4

Stage Out

5

405 nm Laser (Digital)

6

488 nm Laser (Digital)

7

561 nm Laser (Digital)

8

638 nm Laser (Digital)

The stage control card specified for PLC outputs 3 and 4 is the stage that is used for Z-stacks. This allows stage feedback to dictate when the sample is ready for an image. In our configuration, the X hardware stage corresponds to the Z stage within the software. This can be changed to match your stage setup by editing the following part of the configuration file:

Configuration File
microscopes:
  microscope_name:
      stage:
        hardware:
          -
            type: ASI
            serial_number: 001
            axes: [x, y, z, f]          # software stages
            axes_mapping: [X, Y, Z, F]  # hardware stages