Interactive cell analysis

Mayachitra imago's interactive segmentation method segregates the background from the foreground, given the information provided by the user in terms of mouse-drawn scribbles. All you need to do is to provide a few scribbles indicating foreground (e.g. cells or tissue) and background. The segmentation result is updated dynamically as a scribble is added or removed. imago computes the properties of individual cells such as area, perimeter, and average intensity.

First, double click an image to open it in imago's image viewer. Click Cell analysis from the left pane of the image viewer. The cell analysis wizard will appear.

imago's cell analysis tool is incredibly easy to use. Cell analysis is done in three quick steps!

Step 1. Choose a segmentation method

You can use either imago's Scribble segmentation method or a simple thresholding method to segment cells from the selected image.

  1. Scribble segmentation: Use a segmentation method based on scribbles. Cells are segmented from the background based on scribbles you draw on the image.
  2. Thresholding: The simplest method of image segmentation. During the thresholding process, each pixel in an image is marked as an "object" pixel (e.g. cell) if its value is greater than a specific threshold value (assuming an object to be brighter than the background) and as "background" pixels otherwise.

Click Next.

Back to top

cell counting with a mask

Step 2. Apply a segmentation method.

Scribble segmentation

First select a single channel you want to work on.

  1. Foreground brush: Scribble on the foreground (e.g. cell) of an image.
  2. Background brush: Scribble on the background of an image.
  3. Eraser: Erase the scribbles using foreground/background brush.
  4. Options:
    Fill hole: When this is checked, the hole in an individual object is converted as a part of the object.
    Brush/Eraser size: Adjust the size of brush/eraser.
    Foreground color: Change the color of foreground brush.
    Background color: Change the color of background brush.
  1. First click the foregorund brush and scribble on a cell that you want to segment. After scribbling, imago will ask you to scribble on the background.
  2. Click the background brush and scribble on the background within the image. imago will show you the segmenation result immediately.
  3. Continue to add or remove scribbles for foreground/background until you are satisfied with the result. Notice that there might be some falsely segmented regions. These will be modified in the final refining step. When you like the results, click Next.

Thresholding

  1. Select a single channel you want to work on.
  2. Define the "threshold value" that is used to convert individual pixels within an image to forground/background.

Back to top

Scribble more

When the scribbles you drew are not enough for applying the segmentation method, imago will ask you to scribble more.

Draw a cell by click, hold, and drag

Step 3. Refine the result

You can refine the results using the brush and eraser.

  1. Click the brush to add foreground region. Drag on the foreground region that you want to add.
  2. Click the eraser. Drag through the area you want to erase.
  3. When you like the results, click the Apply.

imago computes the properties of individual cells such as area and average intensity from the segmentation result. imago shows the summary of cell counting in image analysis history. When you click Analysis of details in the right side of the history, area and average intensity of individual cells in each channel are displayed.

image analysis history

Back to top

Step 3: refining the cell counting result based on intensity

Image analysis history.

imago keeps the history of cell analysis. Do you need to look for the image plane with a cell analysis result in your stack image? When you click the list from the image analysis history, imago will take you to the specific image with the selected cell counting result. Moreoever, when you click the button next to each cell analysis in the history window, you can refine the segmentation result again.

Search by cell segmentation results.

Do you know you can search images based on cell analysis results? imago's powerful search can help you to find images by the cell analysis results. For example, you can find all images from your album with more than 400 cells.

Search by analysis result

How to count cells automatically

Getting started