SRS image-stack series workflow

Purpose

Use the SRS image-stack series workflow to collect image stacks using systematic random sampling (SRS). You can then use these image stacks with unbiased stereology probes such as Optical Fractionator, rather than conducting a stereological study on live-camera images (see Counting offline after an SRS Image Stack acquisition).

This is useful when:

  • You want to minimize fluorescence-signal bleaching.
  • You have tissue labeled with more than a single fluorophore that you want to compare.
  • You want to archive the image stacks.

Before you start

Procedure

  1. Set up the slide at the desired magnification on a calibrated system.
  2. Click Acquire>Display>Live Image to view the tissue on the screen.
  3. Adjust settings to optimize the display of the tissue (i.e., adequate white balance, light, background, etc.).
  4. Click Acquire>Workflows>SRS image stack series.
  5. Follow the workflow steps.

Workflow overview

After the SRS acquisition

Before opening your data file:

  1. Go to File>Preferences and select the Images panel.
  2. Turn off (uncheck) Zoom to fit on load.
  3. Turn on (check) Remove off-screen image stacks from memory.

Many users combine SRS image stacks with the Optical Fractionator to count cells (see Using Optical Fractionator to count offline after an SRS Image Stack acquisition ).

When counting:

  1. Go to File>Preferences and select the Movement panel.
  2. Turn on (check) focus with mouse wheel and set the Z distance per wheel click equal to the distance between images in your image stack. This will enable you to focus with the mouse wheel instead of the page up/page down keys.

Try to avoid using the Image Adjustment window – making changes to each stack is time consuming. If you need to use it, remember to save every few sites (otherwise, the software will keep unsaved images open in memory, slowing the system down if you have many sites).

If you are struggling with the automatic zoom feature (that is, you have to zoom out at each site to see the counting frame), contact us.