Using Thresholds to Measure and Quantify Cells in Image J


The Cell Division Lab

I often get asked how to uses Thresholds to measure things in Image J.

There are some great guides on the web explaining how to use Thresholds in Image J, and here are a few that are well worth checking out [Link1][Link2].

Below are some of the Basic Steps for using Thresholds:

  1. Open your image and duplicate it (Image>Duplicate)
  2. On the duplicate go to Image>Adjust>Threshold
  3. Play with the sliders until all of your cells are red.
  4. Click ‘Apply’
  5. You should now have a ‘binary’ black and white image
  6. Now go to menu Process>Binary and select ‘fill holes’
  7. You may also want to select erode, dilate, open or close to optimise the binary image so that you have nice solid filling of your cells.
  8. Now go to menu Analyse>Set Measurements. Select all the things you want to measure.
  9. Critical steps: make sure that you select your original image…

View original post 149 more words

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About celldivisionlab

Head of the Cell Division Lab at the Garvan Institute of Medical Research.

3 responses to “Using Thresholds to Measure and Quantify Cells in Image J”

  1. creativebiolabs says :

    Thanks for sharing the detailed steps for using thresholds. It’s just great!

  2. Jordan says :

    Great step by step guide here. It’s important to know how to use thresholds. Thanks so much for sharing this!

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