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Technology Development Group

Hydrodynamic DNA Shearer

Plaque Picker

High Capacity Shaker

Template Preparation Machine

Flow Through Micro-Centrifuge

Plasmid Preparation Machine


Capillary Electrophoresis

Oligonucleotide Synthesizer



Plaque Picker

Plaque Picker The picking of isolated viral plaques or bacterial colonies has traditionally been one of the most tedious and time consuming tasks associated with shotgun sequencing. We have developed a picker capable of processing 1 input dish in ~3 minutes. Furthermore the picker is equipped with plate handling servers which allow the instrument to process up to 80 input dishes without any human intervention. Assuming that the input dishes have an average density of 200 plaques/dish, this should provide adequate plaques/colonies to innoculate the 168 output microtiter plates that are contained in 6 cassettes on a server carousel. Including loading times, this instrument should be capable of handling 10,000 daily samples in roughly 5 hours.

The picker features a rotating turret of tungsten needles. These needles are cleaned in a water jet station and heat sterilized in a small furnace. High throughput is achieved by performing the various steps in parallel. These steps are: 

  1. Wash needle in high pressure water jet.
  2. Sterilize needle in furnace.
  3. Dip needle into plaque/colony.
  4. Plunge needle several times into well containing sterile growth medium.
The input dishes are imaged with a CCD camera and the images are processed using a PC. The instrument operates in two distinct modes: plaque picking mode and colony picking mode. When picking m13 plaques, the input dishes are backlit using a collimated light source. Plaques are revealed as bright points against a dim background of scattered light. A red filter is placed over the camera so that blue plaques from ß-galactosidase selection show up as dark objects which are easily rejected. When colonies are being picked, the dishes are lit from above against a dark background. Again, a red filter is used to distinguish between blue and white colonies. 

The optimization of the dish lighting reduces the challenge of automatically finding the isolated plaque/colony positions. Images are background subtracted to remove any lighting or agar non-uniformities and then features are selected based on brightness, roundness, blueness, and separation from other features. All of these analysis parameters are under operator control through a graphical user interface, allowing efficient recovery of uncontaminated plaques/colonies. Under typical operating conditions, approximately 90% of good plaques/colonies are recovered while > 95% of blue plaques/colonies are rejected and < 3% of the selected innoculations may be of mixed population or sterile. 

While commercial plaque/colony pickers have recently become available, the principal advantages of our system include increased throughput, and, more importantly, greater volume of plates handled without user intervention. This instrument is currently in production operation. 

This instrument is now available through Genemachines. For information call them at 650-508-1634 or e-mail them. 

The plaque picker drawings are now available!

Download the Indented Parts List (RTF) or Indented Parts List (ASCII text).
Download the Drawings as a zipped set of .DXF files.

Contact our Office of Technology Licensing for access to the software.


Plaque Picker Image
Full sized Picker Image
Input Dish
Input Dish Image
Input Dish Movie
Carousel Server
Server Carousel Image
Server Carousel Movie
Rotating Turret
Rotating Turret Image
Rotating Turret Movie
Parallel Turret Steps
Parallel Turret Steps
Sterilization Steps
Sterilization System Image
Sterilization System Movie
Small Furnace
Small Furnace Image
Picking Plaque
Picking Image
Picking Movie
Needle in Growth Medium
Inoculation Image
Inoculation Movie
Processed Input Plate
Processed Plate Image
Needle in Growth Medium
Needle in Growth Medium
Plate Server Movie
Graphical User Interface
Graphical User Interface

Staff | Instruments & Protocols | Automated Sequencing System | Functional Analysis | Software Development
Stanford Genome Technology Center:
Technology Development Group
855 California Avenue | Palo Alto, CA 94304 | Phone: (650) 812-2007 | Fax: (650) 812-1975