Microplate Scanning - Basic

Source Code
Category: Microscopy
Microplate
Python
June 12, 2023

Microplate Scanning - Basic

By Andrew Lau and Mike Fussell

This example script demonstrates how to set up a Zaber motorized microscope stage to scan ANSI standard microplates with 96, 384, and 1536 wells.

Wellplate

Hardware

This script is designed primarily for the ADR (linear motor) and ASR (lead-screw) families of motorized microscope stages, but can be readily adapted to work with any modular XY stages by Zaber Technologies.

Dependencies

The script uses pipenv to manage virtual environment and dependencies:

python3 -m pip install -U pipenv

The dependencies are listed in Pipfile.

Configuration

Edit the following constants in the script to fit your setup before running the script:

  • SERIAL_PORT: the serial port that your device is connected to. For more information on how to identify the serial port, see Find the right serial port name.
  • DEVICE_NUMBER: the order that the controller or stage is plugged into the device chain. For example, if it is the first and only device in the chain then use the number 1. Check the device numbering by opening Zaber Launcher to view the devices connected to a serial port.
  • ROW_HOME_OFFSET and COLUMN_HOME_OFFSET: the offset in millimeters from the home or zero position of both axes to the edge of the well plate.
  • PLATE_TYPE: number of wells in the standard ANSI microwell plate. Use the string "96", "384" or "1536".

Running the example script

To run the script:

cd src/microplate_scanning_basic
pipenv install
pipenv run python scanning.py

Scanning Patterns

The script gives example of three different scanning patterns:

  • sequential(): Scans each row in the same direction. When a row is done, advance to the next column and scan the next row in the same direction.
  • fastest(): Scan the first row in one direction. When the first row is done, advance to the next column and scan the second row in the opposite direction. The advantage over the sequential() method is that less time is spent back-tracking after finishing one row.
  • random_access(): Generate all the coordinates to visit, then shuffle them before visiting each well in a random order, but only visiting each well once.

Tasks to perform at each well

The scanning routine calls the function do_task(*args) each time it visits a microwell. The user can edit the function to do a variety of tasks such as:

  • turn on illumination or change filter cube
  • call auto-focus algorithms to find the sample
  • call third-party camera API to take an image
  • activate pipetting robots to dispense reagents
  • control other motion axes to interact with the sample (i.e. single cell picking)
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