Automatic nuclei detector

Cell counting is a common task in cell biology research. Mayachitra imago's automatic nuclei detector is a powerful image based cell counter. It automatically identifies nuclei's centroid locations from the selected image and provides you the total number of cells and their location information.

First, double click an image to open it in imago's image viewer.

Click Nuclei detector Resizing from the left pane of image viewer. The cell counting wizard will appear.

imago's nuclei detector is incredibly easy to use. Cell counting is done in three quick steps!

nuclei detector wizard

Step 1. Specify the region to count cells.

You can apply the nuclei detector to either part of an image or the entire image.

  1. Entire image: Use an entire image to count cells.
  2. Mask image: If you have already created a mask image, a black and white image to indicate the region of interest, you can select a mask image from your hard disk.
  3. Mask annotation: Create a mask using imago's polygon annotation tool. Select Draw mask and draw a polygon on the image and double click to finish the drawing. The boundary of a polygon will be displayed with a red dotted line. If you have multiple masks on the image, click Select existing mask and choose a mask that you want to use. Then the boundary of the polygon becomes a red dotted line. Learn more about how to create a mask using annotation tools.

Click Next.

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cell counting with a mask

Step 2. Choose a cell size.

You can simply draw a circle around an example cell on the image.

  1. Position the mouse pointer around an example cell in the image
  2. When you click an example cell, imago will show you a circle and the current location of the preview window. Hold your click and drag the mouse to adjust the size of the circle. You can also adjust the size of the circle by dragging the boundary of the circle. The results are instantly updated in the preview window.
  3. Check the results from different locations by simply clicking the inside of the circle and dragging to a different location.
  4. Notice that there might be some falsely detected cells. These will be discarded in the final refining step. When you like the results, click Next.
  1. When this is checked, imago will search for darker cells instead of bright cells (e.g. DAPI stained cells).
  2. Preview window: The preview window will show immediate effect of the current cell size without actually applying it to the entire image. The location of the preview window is displayed on the image as a yellow rectangle. You can click the preview window on the image and drag it around to see the effect on different locations.

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cell counting with a mask

Draw a cell by a click, hold, and drag.

Draw a cell by click, hold, and drag

Adjust cell size.

Move the mouse over the boundary of a circle, the mouse pointer will change to mouse-pointer-adjust, then drag the boundary of the circle to change the size.

Step 3. Refine the results

You can refine the results based on intensity.

  1. Move the slider to get satisfying results. imago will exclude detected cells with intensities lower than a certain value.
  2. When you like the results, click the Done.

imago shows you the summary of cell counting in image analysis history. When you click Analysis of details in the right side of the history, total count, area, density, the parameters, and the XY coordinate of each detected cell isdisplayed.

image analysis history

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Step 3: refining the cell counting result based on intensity

Image analysis history.

imago keeps the history of cell counting. Do you need to look for the image plane with a cell counting result in your stack image? Click the list from the image analysis history, imago will take you to the specific image with the selected cell counting result.

Combine a result with manual counting.

You can move, add, or remove cell locations with imago 's graphical annotation tool. imago also keeps track of the history of modification. In order to delete one, select a centroid location that you want to delete, and right click to access a menu, and then select Delete. You can also add additional centroids' locations. Select any detected centroid and right click to access the contextual menu Continue. Once Continue menu is selected, you can add missing centroid locations. Note that your manual editing results are updated instantly in the table.

Search by the cell counting result.

Do you know you can search images based on cell counting results? imago's powerful search can help you to find images by cell counting results. For example, you can find all images from your album with a cell density larger than 1000 cells/mm2.

Search by analysis result

How to segment cells automatically

Getting started