1/20/2023 0 Comments Imagej colony counting![]() ![]() Although a number of such systems exist, they all focus on enumerating colonies and not on analysing the colony size. Such analyses are largely facilitated by computerised image analysis systems. Moreover, it is often interesting to quantify the size of individual colonies. In large experimental setups, counting of colonies by eye is tiresome and prone to bias. The app can also automatically average a count across a set of plates.The clonogenic cell survival assay is a basic method to study the cytotoxic effect of radiation and chemical toxins. You can then refine the count by marking missed colonies or masking out false positives. Take a picture of your plate and the app will automatically count the number of spots. This handy app costs only $3.99 and is simple to use. Promega’s Colony Counter AppĪs if your iPhone hasn’t already become an indispensable part of your personal life, it can now be used for colony counting thanks to the Colony Counter App developed by Promega and available at the iTunes store ( ). One word of caution: automatic counters can be led astray by imperfect agar, debris, unusual colonies or plaques or even writing on the plate, so it is always wise to validate the system. Basic models just count spots, while fancier models with high-res color cameras can count spots, measure zones of inhibition and provide information on size and shape of the spot. Automatic counters can range in cost from $4200-15,000. If you are faced with hundreds of plates to count each day, an automatic counter can make your life a lot easier. Once an appropriate image of the plate is captured, free software, (such as MATLAB which is available at can be used to identify and count circular spots. Other labs have used flatbed scanners to image plates. Essentially you only need something to hold the plates, a camera, a light source and a computer. If you are mechanically-inclined, you can put together your own automatic counter, as described by Brugger et al. For a small investment (To increase accuracy, count the plate, rotate 90 degrees and count again or add a second person to confirm each plate’s tally.Use a handheld clicker-counter to help you keep track.Use a sharp-tipped marker to mark each colony/plaque as you count it.Divide the plate into grids for ease of counting.Putting the plates on a light box can be very helpful. Sit in a comfortable seat with lighting that illuminates the colonies/plaques the best.If you are counting manually, make life a littler easier for yourself: If you can’t predict the results of your experiment, plate several different dilutions- it will save you time in the end. Likewise, having only one colony/plaque to count is meaningless. For plaques, make sure you have a nice even monolayer of cells with no clumps.Įven with the aid of technology it’s impossible to count hundreds of colonies/plaques in one dish. Make sure your agar plates are smooth and free of bubbles. It may seem silly, but starting with nice plates can make all the difference in an accurate count, whether being done by human or machine. Below is a list of tips and a summary of available technologies for making sure you get accurate results efficiently. Whichever way you approach colony/plaque counting, we are here to help. However, sometimes you are faced with mountains of plates to count and throwing some money and technology at the assay can significantly increase your speed (and save your poor eyes!). It can also be one of the cheapest when performed manually. …but a simple oneĪ good thing about colony counting is that it is probably one of the simplest assays you will ever perform. Necessary because many experiments have an endpoint that requires determining the number of bugs present in a sample evil because it can be tedious work that strains the eyes. I consider colony/plaque counting one of the necessary evils of working with microorganisms. Have you ever emerged from the lab, bleary-eyed, blinking dazedly at the sun after spending hours hunched over a lab bench counting endless bacterial colonies or viral plaques? A necessary evil… ![]()
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