Controlling the microscope

From Endrov

Contents

Why

You can use Endrov to control your microscope. This has several advantages over commercial software:

  • The latest software features are available without having to pay for upgrades
  • It's free software that you can hook up to an increasing number of microscopes; a single familiar environment
  • Since it is free, other people can use the same system with the same settings to reproduce your results
  • No limit to how much you can extend the functionality; the hardware will be the limiting factor, as it should be
  • You can make use of the sophisticated Endrov data model to analyze images on the fly, and act upon the data
  • Save in any supported image format, on any image server, or add your own

Setting up the basics

See Configuring the microscope.

The stage can also be controlled using a gamepad.

A first taste of microscopy

All properties (settings) of the microscope can be reached by opening the Property window (Windows . Recording . Property). This window has two tabs: "All" and "My properties". The first tab contains every property your hardware provides, which is more than you conveniently can work with. Your first task before doing serious acquisitions is to set up your personal list of properties (see later section). Some of the things you can first try to do are:

  • Turning your light source on/off
  • Turning your shutters on/off
  • Changing filters
Hwpropwindow.png

To see what is happening in the microscope, use the Live Window (Windows . Recording . Live View):

Camlivewindow.png

A single image can be acquired from the camera using the button "Snap", or by checking "Live" to obtain a continuous stream of images. Images captured using other displays can also be displayed in realtime by toggling the "Update" checkbox.

A histogram showing the intensities is shown below. These values are mapped to the screen using a lowest and highest limit, displayed as vertical lines. If you have trouble seeing the image, make sure these limits are set correctly. Making it "auto" will ensure that the entire image is fit within the limits. Pixels which are out of range above are marked red while those which are below the lower range are blue. This can be used to find, in particular, pixels which are saturated. If pixels are saturated you should either lower your exposure time or brightness, as saturated images cannot easily be quantified and you are losing information.

Single snapped images can be stored in a file using the dialog at the bottom. You need to first create a new file (File -> New) and choose it. The name is the name of the series, e.g., if the name is "im" then images will be called im00000000, im00000001 ... and so on.

The XY-stage can be moved by holding the right mouse button and dragging the mouse. To move in the Z-direction, use the scrollwheel. For the movement to work optimally, you need to have configured the resoluton.

Grouping settings

It is not possible to work with the entire range of settings all the time - the microscope has to be simplified into a few imaging modes (such as for different fluorophores) and a few commonly changed options (such as exposure time). Endrov supports this as "groups" using the Property Window.

Before creating a group, consider what you need to know to know to set the microscope for a certain mode. These are just some suggestions:

  • active filters
  • prisms
  • choice of camera
  • light sources, on/off
  • brightness

To create a new group, press "New group". Add all the properties you think should be included and give it a name (for example "channels"). Next, for each mode, set up the requires settings. Then press "+" for this group to record the settings, and give it a name. Verify that the group works by choosing different modes.

Moving on to serious use

Before doing real microscopy, you should calibrate your resolution.

Then learn to use The multi-dimensional acquisition window, the work horse for most applications.

Finally, if you work with large plates, learn to use the The plate positions window. The The plate overview window is also useful to keep track of where you are.