Measuring sample area

Shebar
Shebar
in Image-Pro Plus General Discussions
Hello. I am a new user of image-pro plus. I work with the histology samples and my project involves measuring sample area (entire sample). I measure sample area manually and it takes forever..., just wondering maybe there is some automatic features that I can use. Thank you in advance for your time. Look forward for some ideas :) 

Best Answer

  • mbatchelor
    mbatchelor
    Answer ✓
    2016-11-28-103440

    Shebar --

    The SCREEN CAPTURE is a composite of multiple SCREEN CAPTURES and I accidentally generated an image of the COUNT / SIZE DIALOG BOX with both the BRIGHT and DARK RADIO BUTTONS ENABLED.  That should just be the BRIGHT OPTION.  I apologize for the confusion this caused.

    The steps / settings that create UNTITLED11 from B.TIF MASK are

    COUNT / SIZE +
        AUTOMATIC BRIGHT THRESHOLD
        APPLY FILTER RANGES
        OPTIONS +
            AS SHOWN
        SELECT MEASUREMENTS +
            AS SHOWN

        COUNT BUTTON

        IMAGE MENU +
            MAKE MASK

    After you do this, you should have a "clean" image of your TISSUE AREA.

    You can extract your TISSUE AREA MEASUREMENT from your equivalent of the B.TIF MASK image but sometimes it is nice to clean up the mask.

    I hope this information is helpful.

    -- Matt

Answers

  • mbatchelor
    mbatchelor
    Shebar --

    I think we (the FORUM) need to know a bit more about your challenge to advise you properly.

    If you can provide a SAMPLE IMAGE or a SAMPLE IMAGE SET that illustrates your challenge, I'm sure that we would be able to help you.  I believe that the FORUM will accept JPG IMAGES and TIF IMAGES.

    Also, if you have information about the CALIBRATION for your SAMPLE IMAGE(S) (ex. um/pix), that would help us advise you.

    I hope this information is helpful.

    -- Matt
  • Shebar
    Shebar
    Thank you for your answer. I'll try to Provide more information on my problem. I need to measure the whole area in provided sample. To measure the sample area I need to define margins of the sample (as in the second pic marked black). So I mark it manually and then Image Pro counts area for me which I can export to excel. Marking manually those little notches on sample consumes lots of time, especially if i have lots of samples. So, my questions maybe there is automatic feature which may mark margins and count area for me. Thank you for your time and answers in advance.







     
  • mbatchelor
    mbatchelor
    edited November 2016
    Shebar --

    The SAMPLE.PNG image that you posted is very low resolution but I have used it to illustrate one of the ways to address your imaging challenge.

    Attached, please find

        2016-11-21-161826.jpg

    In this SCREEN CAPTURE / ILLUSTRATION image:

        A = ORIGINAL IMAGE that is SMART THRESHOLDED to obtain IMAGE B
        B = MASK of SMART THRESHOLD applied to IMAGE A
        C = ORIGINAL IMAGE that is MANUAL MEASURED to obtain IMAGE D
        D = MASK of MANUAL AREA obtained in IMAGE C
        E = .5 * IMAGE A
        F = E + D
        G = DUAL THRESHOLD of IMAGE F

    Results in EXCEL (far right box) can be achieved with:
        1) IMAGE B (GREEN OVAL) and IMAGE D (GREEN OVAL)
        2) IMAGE G (GREEN OVALS)

    I hope this information is helpful.

    -- Matt

    *-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-




  • Shebar
    Shebar
    Thank you for your answer. I'll try it. Just I work with Image pro plus, not premier. Are these functions available and the same on Image pro plus?

  • mbatchelor
    mbatchelor
    Shebar --

    I apologize . . . I did not notice that this question was relating to IMAGE-PRO PLUS and not IMAGE-PRO PREMIER.

    The only feature that I was suggesting that PREMIER has that PLUS does not is the SMART THRESHOLD.

    I have created another FLOW CHART type image that shows a PROCEDURE that will take your ORIGINAL IMAGE and turn it into a TISSUE AREA MEASUREMENT in IMAGE-PRO PLUS.

    The other parts of the PROCEDURE shown yesterday are supported by FUNCTIONS and FEATURES within IMAGE-PRO PLUS.

    I hope this information is helpful.

    -- Matt


  • Shebar
    Shebar
    Thank you so much. It's very helpful. Can't wait till to tomorrow to try.
  • mbatchelor
    mbatchelor
    Shebar --

    Super.

    If these steps result in the analysis you need, they can be automated with an IMAGE-PRO PLUS MACRO so that they can be executed quickly and with very little user input.

    -- Matt
  • Shebar
    Shebar
    One more question. I've just noticed that area is measured in pixels, is it possible to measure mm?

  • mbatchelor
    mbatchelor
    Shebar --

    Certainly.

    CALIBRATE your IMAGES using the features in

        IMAGE-PRO PLUS + MEASURE (MENU) + CALIBRATION + SPATIAL

    and then any measurement extracted from the image will be calibrated (if it is appropriate).

    -- Matt
  • Shebar
    Shebar
    Thank you so much for your help. 

  • Shebar
    Shebar
    Thank you for your help, still have some questions. I've failed to convert pic in third step (attached. picture). Could you write what exact steps I missing to convert to it. 
    Another question is when I select counting it doesn't give me a choice of both, how is showed in our picture (it gives either automatic bright objects or dark). How you would recommend to solve this problem? 
    When I do final counting area data is expressed in many numbers, to get the final area count, i need to sum the numbers. In your picture data is expressed as one parametre, so maybe I do something wrong. Maybe have some ideas? Thank you in advance for your help.

  • Shebar
    Shebar
    Thank you, I will try. 

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