Imagej colony counting free#

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.

Imagej colony counting free#

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. A colored number corresponding to the type you are counting will be displayed on the image every time you click, and the corresponding counter is updated.Īdd the following macros to ImageJ/macros/StartupMacros.txt, restart ImageJ, and you will be able to change the counter type by pressing '1', '2', '3', etc.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… Select the type you want to count, and count by clicking on the feature in the image. Note that at any time you can add types or remove them. Click initialize, now you are ready to count features. Open the Cell Counter plugin and the image/stack you want to count (if the Cell Counter plugin is already open you don't need to open a new instance).

Measure.: Measures the pixel value at each marker and displays a result window showing: Type - Slice - X coordinate - Y coordinate - Pixel Value.

Export Image: Makes a copy of the counter image with the markers written on it (only the current slice is copied in case of a stack).

Load Markers: Loads stored marker data from an XML file - Only available when running java 1.4 or higher.

Save Markers: Exports the marker data to an XML file - Only available when running java 1.4 or higher.

In case of a stack the counts per slice and the totals are displayed.

Results: Shows the counter results in the ImageJ results table.

When checked, the marker of the currently selected type closest to the mouse cursor will be deleted when you click.

Delete mode: toggles between insert and delete mode.Initialize: Initializes the current image or stack for counting, this will create a duplicate image/stack titled 'counter window' - when keep original is checked, the source image remains open.Opens off-screen on 1024 pixel wide and smaller monitors. May not work correctly after using Load Markers to load more than 8 counter types from an XML file.