• 00:00 1.
    Counting Cells with ImageJ
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Counting Cells with ImageJ
Duration: 05:06, Browse: 3058, Last Updated: 2019-08-13
Keep in mind that ImageJ processing is not perfect. However, the error of missing cells may be "corrected" by the error of including some noise.
Keypoint
  1. 1.

    Open ImageJ

    08996e5f14518f31cea5112bd294c633.png

    File à Open à cell count.jpg

    9bdf94395d1aa1035953b797b2c9814f.png

    Click “開啟(O)”

    85290cf2ec5a4c7998aabd592101b0d6.png

    Edit à Options à Conversions

    bab8d3f9931479c417359ab64a51c35d.png

    Check “Scale When Converting”

    11bc60a316c36dfd5dbccb496935ec4d.png

    Click “OK”

    75000a394354554eaa61d295e75cb263.png

    Image à Type à 16-bit

    d6fb88fd7e14a4558edb04a66aa8ebd9.png

     

    Image à Adjust à Threshold

    b6d155f36bcf488eaa085877d24f5acb.png

    758e2a05a02b6f21c1d0b9ed9a7b96e8.png

     

    Adjust threshold until you are satisfied

    Click “Apply”

     

    2e28a77933a91238ec68ee9a7ffd36fb.png

    * To fill the hole in cells

    Process à Binary à Fill Holes

    * To separate two overlapping cells,

    Process à Binary à Watershed

     

    378e554de044b081465d97cff3216947.png

     

    eaf46d3aca7788479fb00177d9c784f2.png

     

    Analyze à Analyze Particles

     

    3ffc725d597b495bc5bf452a45062ce4.png

     

     

    30b491884efa448d4726196256037b9a.png

    Size (pixel^2): to count all particles, 0 – Infinity

    Circularity: 0.00: a straight line; 1.00: a perfect circle;

     

    Check cell size and circularity

     

    Click “OK”

    56693600c02346c314b2f679052931d8.png

    Cell number is 68 at current setting.

    However, check Areas in Results windows, some noises are included. So, change area size

    Analyze à Analyze Particles

    2985a44f43b41e5cecee36adcceef51e.png

    Show: outlines

    Size (pixel^2): to count all particles, 6 – Infinity

    Click “OK”

    273964bab94eeaaa8b3383c65ae8c4c1.png

    Show: mask overlay

    3c28ace3b82ed680fffcb00e3b2159fb.png

    Cell number from 68 à 64

  2. 2.
    Count cells manually

    Open ImageJ

    c450a2fe66aad93ef2fcc0e139ac70c5.png

    File à Open à cell count.jpg

    08bd4830fe4e1be363505c957bd7d9dd.png

    Click “開啟(O)”

    9ba059c18f7b9e5974c6dc48aff489ce.png

     

    Plugins à Analyze à Cell Counter

     

    a7ad62b17c2ba1f837fad16e1306cca4.png

     

    9ffdf8eaf4bc90cd7a456d5b0a54527d.png

     

    The current example contains only one cell type, so click “Remove” to remove other cell types.

    Click “Initialize”

    Check “Keep Original”

    c82a32b92bd29007dd249a6b67eee802.png

    Click “Type 1”

    Click on cells to count

    5c92a863fe42c87cbb2ab7ee09af0cdf.png

    Cell number is 63

     

    Location
    Folder name
    ImageJ
    Author
    賴亮全
    Branch
    賴亮全教授
    Created
    2019-08-13 14:29:15
    Last Updated
    2019-08-13 14:40:30
    Duration
    05:06
    Reference
    2
    Source
    https://www.youtube.com/watch?v=D1qBaFwuF4E