Colony Counting & Analysis: PhenoBooth

Counting E. coli colonies is easy. Counting pseudo-invisible, sausage-shaped colonies and excluding yellow circular ones isn’t. Oh wait, yes it is, I have a PhenoBooth.

Colony Counting petri dish 

What is it?

The PhenoBooth Colony Counter is a fast, super-easy to use, closed-chamber Colony Counter for imaging and analysis of colonies on agar.
It uses a scientific grade, HD camera and 4-channel, flat-field SpectraStar™ incident and transmission illumination to capture high-resolution colony images from Petri dishes and SBS plates.

How does it work?

Insert a Petri dish with visible bacteria, yeast or other microorganism into the input tray; select your preferred wavelength; autofocus and capture your plates in seconds. Filter for properties of interest just once; hit ‘Batch Analyse’ and walk away as PhenoBooth automates the tedious analysis across all of your plates with a single click.
Colonies can be filtered by size, colour, circularity and brightness. Applications include Colony Counting, Growth Curves, Fluorescence (BFP/GFP/YFP/mCherry*) Detection, Serum Bactericidal Assay, Opsonophagocytic Killing Assay, Spiral Plate Analysis, Single Radial Immunodiffusion and Ames Testing.
*mCherry available with PhenoBooth Cyan lighting option. The PhenoBooth is not a microscope! It is a macroscopic CCD imaging workstation. As such it will not detect sub-cellular or low levels of expression.

Why do I need it?

  • Pick the hits that interest you – Filter colonies by: size, colour, circularity and brightness
  • Get the best results – Second to none. Top quality illumination and photography for top quality analysis
  • Analyse anything – Select from any of 3 SpectraStar™ incident illumination channels: white, blue and ultraviolet or 1 transmission illumination channel. Also accepts standard 25mm colour filters
  • Remove variables – Batch processing and analysis of your plates with a single click
  • Stop wasting effort – Nothing compares. E. coli, fungi or phage plaques: detect it all. Detect every colony, every time, even at 6,144 array density
  • Future-proof your lab – Application-specific software packages, such as Colony Screening or Colony Picking are integrated seamlessly with additional plug-ins available for advanced functionality



Colony Size
Colony Circularity
Colony Coordinates Export
Colony Picker Integration
Gene Mapping
Heatmap Visualisation
Control vs. Experiment Comparison (in replicate)



What plates can I use with PhenoBooth?

The PhenoBooth accepts Singer PlusPlates and any SBS-format rectangular plates. Want to colony count on 90mm Petri dishes? We’ve got an adaptor for that too.


How many plates does PhenoBooth take?

PhenoBooth takes one plate at a time to ensure that every plate received identical lighting and exposure setting, which is necessary to maximize data quality and save time on downstream analysis.


How fast is PhenoBooth?

It takes PhenoBooth only 5 seconds to image one plate.  This means that you could image up to 720 plates in an hour.  It is that fast!


Does it come with a stacker?

No, it doesn’t.  Because PhenoBooth is so fast, you don’t need to waste time loading plates onto a stacker.


What type of lighting is available in PhenoBooth?

PhenoBooth offers two types of lighting options: transmitted (back) light to maximize contrast between colonies and background, and incident (top) light to capture colour. The PhenoBooth is available in two different LEDs set-ups. The standard PhenoBooth includes UV, blue and white light. The PhenoBooth Cyan option includes cyan, blue and white light.


What is the Colony Picking Platform?

The Colony Picking Platform is made up of the PhenoBooth, the ROTOR HDA and The Stinger. Image randomly arrayed colonies using the PhenoBooth, then filter and select colonies of interest using the Colony Picking software package. The colony coordinates can be exported and loaded into the ROTOR HDA screening robot and picked into an array by The Stinger single colony picker head.

What exactly does the software do?

PhenoBooth’s software is a powerful solution with an intuitive UI for colony measurements and analysis. It consists of 6 fully integrated steps, including Image Acquisition, Pre-processing, Detection, Filtering, Analysis and Visualisation. Fully automate your favourite workflow.


What colony features does the PhenoBooth measure?

The PhenoBooth measures most phenotypes, including size, colour, circularity and brightness. If you want to make a measurement that doesn’t currently exist, just contact us and we’ll write the plugin!


Can the PhenoBooth detect sub-cellular or low levels of fluorescent expression?

The PhenoBooth is not a microscope! It is a macroscopic CCD imaging workstation. As such it will not detect sub-cellular or low levels of expression. The in-house strains used to successfully test PhenoBooth’s fluorescence detection have a fluorophore molarity of 1.84E-30 nM per cell. As such we cannot guarantee fluorescence detection below this value.


Can I perform data analysis as well?

Absolutely! The PhenoBooth is your one-stop solution for SGA analysis. It measures and normalises colony features, compares measurements on experimental and control plates, identifies and presents “hits” on a heat map or a chart. In addition, there will be extra plugins and packages available to customise workflow that deviate from standard SGA analysis.


How many software Licenses do I get?

You get three 1-year user licenses as standard! Don’t worry, you’ll still be able to use the PhenoBooth software with an expired license, but will miss out on some additional benefits. Additional licenses can be purchased at any time.


Help! I need PhenoBooth to do THIS for me!

SI constantly makes new software plugins for the PhenoBooth to fulfil different analysis needs.  Please contact us if you have a good idea for what PhenoBooth should do next. We’d love to hear from you! 

Tech Specs

PhenoBooth Colony Imaging & Analysis Technical Specifications

Standard Product Code



Cyan Product Code




L: 30.5 cm x W: 30.5 cm x H: 31.5 cm



22 kg


Power Requirements

100-200V AC 50-60 Hz, Power 60 W


Camera Specifications

Scientific grade, 13MP HD CMOS (5MP plate resolution)

Auto focus lens


PhenoSuite colony analysis software

Touch-Screen MCI

16:9 15.6″ display
Intel Haswell Core i5-4300U
Microsoft Windows 10 Pro 64-bit


Standard Software Package Included

Colony Counting


Colony Picking Platform

Colony Picking Platform

The PhenoBooth can be purchased as part of the Colony Picking Platform which also includes the ROTOR and The Stinger.
Image plates of organisms such as yeast, fungi, bacteria and algae grown on solid or in liquid media using the PhenoBooth. Select hits by phenotypes such as size, circularity, colour or fluorescent intensity. Import this data into the ROTOR HDA and use The Stinger to transfer cells from hits onto solid or into liquid media. See the video



Singer Instruments has a long-standing reputation for fantastic service and support, for which we are very proud. Our motto, ‘a responsibility to science’, extends to our service and support whereby our primary motivation is to eliminate, or at least minimise, your experimental downtime. We design our products for reliability, longevity, speed, and ease-of-use. Our Lab Support packages augment these design criteria by increasing life-expectancy and increasing device reliability with preventive and predictive maintenance. Should any reactive maintenance be called upon, our time, cost and carbon efficient support should get you up and running in the shortest time possible.

Singer Instruments’ products are fully guaranteed against faulty materials or workmanship for one year from the date of commissioning. Should the product be controlled by a computer, the guarantee necessitates internet connectivity for remote access* availability.

Singer Lab Support is an excellent and cost effective service that gives the Laboratory unlimited access to Singer technical experts by phone, email, VOIP or remote access. All requests are entered into the Singer ticketing system that allows both the Laboratory and Singer Instruments to log, track and monitor any reported issues from initial contact through to resolution. While we aim to respond to all queries within 24 hours, our average response times are far less.

Our Singer Lab Support packages come with discounts for multiple years, multiple products and renewals. We offer 2 levels of cover – Lab Support and Lab Support Plus.

*remote access – a highly secure method of allowing a Singer Instruments engineer access to your machine via an Internet connection. Not applicable for all products.


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Consistent Image Acquisition

SpetraStar - Top and bottom Flat Field Illumination


SpectraStar™ technology ensures that every part of the plate is evenly lit without shadows and without external light hazard.

PhenoBooth PhenoSuite feature: Felexible Illumination


Both transmissive and reflective illuminations are available.

Comprehensive Colony Characterisation

PhenoBooth - Colony Imaging & Analysis Software - PhenoSuite Colony Sizing


Scientific grade camera with image acquisition at 2800×1900 with a pixel size of 45µm.

PhenoBooth/PhenoSuite feature: Measure Colony Circularity - High-throughput Screening


Circularity of a colony is a useful measurement for quality control.

Measure Colony Colour


Detect and break down colour components in a colony.

Powerful Data Analysis

PhenoBooth - Colony Imaging & Analysis Software - PhenoSuite 6144-density array


Accurately detect and measure colonies at as high as 6k density.

PhenoBooth/PhenoSuite feature: Normalisation of plate and batch effects


Perform normalisations of various plate and batch effects so that you can get quality data with high confidence!

PhenoBooth/PhenoSuite feature: Scoring for SGA


Powerful plug-ins for SGA analysis are available, allowing you to compare data against control plates and display results as a heat map.

PhenoBooth - Colony Imaging & Analysis Software - PhenoSuite Colony Counting


Accurately count the number of colonies on a plate.

Export Data for Colony Picking


Data export and import is possible at any stage of your workflow.





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