Colony picking is an important step in many workflows, it plays a vital role in early drug discovery and microbial screening and can be the biggest bottleneck in research. An automated colony picker is one of the easiest ways to increase your lab’s productivity; however, buying a colony picker can feel like a big financial decision. Make the right choice for you by taking these factors below into consideration, and decide carefully what features you need, to make sure it will fit smoothly into your lab and workflow.


One of the easiest decisions to make is how many colonies you need to pick a day. Ask yourself how many plates do I have? What is the average number of colonies per plate each day? Am I limited to 8 hours of lab time? Or, could I pair the colony picker with a robotic arm and schedule walkaway time? Making the most of your lab and its assets is important, increase your uptime during the day or overnight too.

Colony pickers are usually advertised by their maximum hourly picking speed, however, super high throughput colony pickers present a higher risk of cell splashing, leading to contamination or inaccuracy. Is it more important to me how many colonies I can pick per hour, or how many I can pick per day? What would the future look like if I could pick colonies for 24 hours and reliably select 10-15,000 colonies in that time?


Consider which organisms you need to pick and whether the colony picker you’re looking at works best for your single, or often multiple microorganism requirements. Make sure it can pick diverse colonies without damaging them, priority features to look out for are: having surface detection on every pick, and a customisable swirling motion to pick difficult organisms.

Consider whether your plate has a single organism growing on it, or, if working with microbiota or other environmental isolates for example, can the colony picker reliably pick a variety of organisms on the same plate? Or, will I have to change between cumbersome, specialist pins for each organism?

PIXL picking

Figure 2. PIXL picking yeast colonies.

Tracking plates and data export

With increased throughput, traceability of plates is important for tracking data. Some automated colony pickers assign barcodes to the plates for end-to-end traceability or are compatible with a barcode reader. Also, consider how colony pickers export data and what format this is in.

Compatibility into workflows with other instruments

If scaling up your workflow to the highest level possible is a priority, and you value walkaway time, consider whether the colony picker is compatible with a robotic arm and how easy integration with other instruments is. Look out for whether the instrument has its own free API (Application Programming Interface) and how thorough the documentation is for it.

Lab space

We all know that lab space is at a premium. A colony picker with a smaller footprint will be beneficial if your lab space is limited and for it to be light enough to be placed onto a standard workbench – check whether the provider recommends (the additional hassle of) ordering a replacement / reinforcing your bench. If you work with anaerobic microorganisms, consider automated colony pickers small enough to be compatible with anaerobic chambers.


Make sure the colony picker can assure sterility throughout the workflow, reusable pin heads cleaned using an ethanol bath come with an increased risk of cross-contamination. Washing cycles can be time-consuming and ethanol poses a significant risk to algae and E.coli samples. Consider the importance of sterility in your workflow; look at automatic colony pickers that use a polymer pin, cut for each pick to minimise contamination.

PIXL Blade & Anvil Kit

Figure 1. PIXL cutting used PickUp Line

User experience

If many different lab users are engaging with the instrument, it is worth considering how easy the instrument is to use and how intuitive the software is. Intuitive software that can be learnt quickly saves a lot of time and reduces downtime when doing maintenance. Nobody wants to buy an instrument that only one person in the Lab knows how to use – this is sadly all too common.

Selection parameters

Automated colony pickers have user-defined selection parameters such as size, colour, shape, proximity, and intensity. What phenotype(s) am I expecting my colonies to express?  Make sure you select a high-resolution colour camera if you need to filter colonies by colour and/or provide colour images for your research. Am I using fluorescent tag proteins? Do I need to filter by fluorescence intensity? Consider if multiple lighting channels would be beneficial. Think about colony pickers that have a good flatness of light for even illumination across different plate types. Would customisable plate sectoring be useful for easy comparison of environmental conditions?

Another consideration when buying a colony picker is the flexibility of the detection parameters. Can it accurately detect organisms beyond E.coli? Such as algae and filamentous fungi? What about diverse plates that have multiple organisms? This flexibility ensures that you can adapt the colony picker to different experiments.


Agar surface detection can be beneficial to compensate for natural variation in agar height; and to regulate the contact pressure applied to all colonies. Make sure the plates you use in your workflow are compatible with the automated colony picker and that it can pick from one plate type to another. Can it handle different plate sizes and types of agar? Can it pick from SBS to MALDI-TOF MS or to PCR plates?

Figure 3. PIXL picking to MALDI-TOF MS plate.

Service and support

Never settle for anything less than world-class reliability and service. If there are many support engineers in your area, what does that tell you about the reliability of the company’s product? Oddly, many companies advertise that having lots of support engineers is a good thing? Challenge this misnomer, expect better.

Consider the maintenance requirements and durability of the colony picker. How often does it need servicing? Are spare parts easily available? Investing in a machine that is built to last and requires minimal maintenance will save you time and money in the long run. Look for companies with a high NPS (Net Promoter Score), where a score over 70 is considered world-class, meaning most customers would recommend the company or product to a friend or colleague. Few support engineers and a high NPS is a great signs that your product will work, this is our number one piece of insider advice from within the industry. 

Improve your productivity and efficiency of your workflows with an automated colony picker that fits well into your lab and can pick your desired colonies. Use the checklist below to help you decide what features are the biggest priorities for your workflow.

Colony picking checklist

  1. How many colonies do I need to pick a day?
  2. How many hours of uptime are available – just 8 hours? Or could I run workflows overnight?
  3. Which organisms do I need to pick?
  4. What phenotype(s) am I expecting my colonies to express?
  5. Would colour imaging benefit my workflow?
  6. What selection parameters do I need?
  7. What plate types do I need to pick from/to?
  8. Would integration with other instruments be beneficial?
  9. How many people need to use the colony picker? 
  10. How much space do I have in my lab?
  11. How reliable do I need the colony picker to be?
  12. What level of support do I need?

Pick 15,000 colonies a day by pairing PIXL with a robot arm for 24 hours of walkaway time, with a less than 0.03% contamination rate and 99.78% pinning transfer efficiency.

Which PIXL setup is right for you?


This easy-to-use, compact bench-top robot is designed for picking and re-plating at densities 96, 384, 1536 and 6144. Using the 6144 RePads.

Precision Microbial Colony Picker PIXL in Anaerobic Chamber.

PIXL with Anaerobic Chamber

A customised anaerobic chamber designed for PIXL with user experience in mind, making integration seamless.


PIXL, is equipped with a automatic door that can be easily integrated with various robotic arm providers.