Parent child app

I am naive to image propramier. 
 I have multiflourescent labelled images with 3 colors whic are imaged   from ZEISS Slide scanner.
I would like to quantifiy the area in Alexa 488 (Hippocampus area), in the same ROI I have to qunatify segmentaion (Alexa 555) andalso  numbers in Alexa 647.
I also need to qunatify the relation between two of the qunatifiations (area to segmentaion).
I would like to know if parent child app would be the best for my qunatification. if yes can I use the readymade app that was already in the App center?
if yes how can I adopt that to my image settings?
I could not find any webinar related to the parent child app.
I would be glad if you can suggest me as soon as possible. I badly need to figure my Quantification soon.
Thanks in advance

Best Answers

  • Accepted Answer
    2017-07-05-094407

    CMS --

    It sounds like you are working with very large (number of pixels) of a relatively small (microscopic) area.

    This usually generates areas which blend into each other and make classifications difficult.

    Would it be possible for you to find a representative section of one of your images that is a reasonable size (maybe 1000 x 1000 pixels) that you could post with a good description of how you would like to measure it with IMAGE-PRO PREMIER?

    Thanks.

    -- Matt


  • Accepted Answer
    Hi CMS,

    You will need to extract the image channels first from the czi file.  You may use any one of the images as the parent image and markup the areas you want to restrict your measurements to.  There is a polygon tool to define the areas.

    Add a child image and set up your segmentation protocol for that image.  It is a good idea to name the what your are analyzing in that image in the segmentation dialog box under Class Name.  All segmentation tools allow you to name the class name.

    Once the setting are correct, press the Count button in the Parent Child App for that image.  Repeat for the other two images.  If you have additional questions, please contact me at jknipe@mediacy.com.
  • Accepted Answer
    CMS,

    The image is still not there. Try to use "Attach file" button to attach TIF or ZIP the file and attach the ZIP.

    Yuri
  • edited July 2017 Accepted Answer
    CMS,

    I'm not sure if I understand all your steps correctly, but I have created a parent-child experiment that handles you images. I assumed that the Green channel (498) is the parent and Red (594) and Cy5 are children. (unzip 3ChannelsCMS.pcp file to any location)
    The project counts the number of Red and White dots in the parent area and reports the count, area and percentage in the output table. 
    I've also attached a video (zipped) that demonstrates how to use the app with your samples.
    If you follow all the steps shown in the video correctly, you should end up with this table:



    Regarding calibration - you must have either a reference object or know pixel size to create calibration. You can check other video tutorials on our website that show how to use Premier in details: http://www.mediacy.com/resources/media


    Regards,

    Yuri
  • Accepted Answer
    Hi CMS,

    the easiest way would be to record a macro that applies calibration to the active image and then call this macro in the beginning of batch processing macro (LoopOn macro). In that case every you image will get calibrated before processing.

    Yuri

Answers

  • Dear Matt,
    Thanks a lot for the reply. 
    Please find the attached tiff file. I could not upload the original CZI file, so attached the TIFF 

    I would like to qunatify the bright green area and then count the cells in the red channel (Cy3) and in CY5 (white cells). I like to have a correlation to the green are a and the red cells in percentage. 
    Hope this helps, and please ask me if needed further information.
    Best,

    2017-07-05-094407

    CMS --

    It sounds like you are working with very large (number of pixels) of a relatively small (microscopic) area.

    This usually generates areas which blend into each other and make classifications difficult.

    Would it be possible for you to find a representative section of one of your images that is a reasonable size (maybe 1000 x 1000 pixels) that you could post with a good description of how you would like to measure it with IMAGE-PRO PREMIER?

    Thanks.

    -- Matt



  • 2017-07-05-172607

    CMS --

    I'm sorry but I do not see the EXAMPLE IMAGE FILE that you mentioned in your message.

    Can you resubmit it please?

    -- Matt
  • Sorry I think there was some issue to attach the files together.

    Pleaae find the images... I splitted the channels and attaching them seperately

  • please let me kniw if you recieve the image.


  • here is one of the image. I am unavble to attach all
  • Fpr the attached images I wanted to quantify the attached  images.  I have to measure area and in that area I count  numbers in gren channel and smart segmentaion in  red channel and count objects in  Cy5 *white dots.

    Please let me know if parent child app would be the right for this_

    I have downloaded the parent child app.

    How can I adopt the app to my quantification

    I also need to have the calibration for this image I can add scale bar to the image and calibrate

    Is it possible to adopt automatically the spatial calibration to all images

    I wanted to have the data file with  area,  total number for green channel and  sum segmentaion for red channel and total numbers  white cy5 channel per  image

    Can you kindly  help me with the steps how I can adopt this parent child app to me  or you think I can write app my own.

    Unfortunaely I have no clue in developing  apps or writing macros

     Please do help me, I have so much data to quantify using image propramier 9.3 version

     

    Thanks a lot,

  • 2017-07-21-101016

    CMS --

    I have downloaded the TIF IMAGES that you posted.

    Super.

    I have opened, rotated, cropped, and overlaid the images as shown below.

    If I understand your request, you would like to know where there is activity in the RED vs GREEN vs BLUE.  Specifically I believe that you would like to know where there is RED within BLUE or GREEN.

    If you will clarify this, I'll be happy to contribute how I would tackle the challenge.

    Thanks.

    -- Matt

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


  • Dear Matt,
    I woud like to know the bright gren area and with this area how many red cels and blue cells are in.
    Hope that helps, 
    Thanking you,
    CMS




    mbatchelor said:
    2017-07-21-101016

    CMS --

    I have downloaded the TIF IMAGES that you posted.

    Super.

    I have opened, rotated, cropped, and overlaid the images as shown below.

    If I understand your request, you would like to know where there is activity in the RED vs GREEN vs BLUE.  Specifically I believe that you would like to know where there is RED within BLUE or GREEN.

    If you will clarify this, I'll be happy to contribute how I would tackle the challenge.

    Thanks.

    -- Matt

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



    CMS,

    I'm not sure if I understand all your steps correctly, but I have created a parent-child experiment that handles you images. I assumed that the Green channel (498) is the parent and Red (594) and Cy5 are children. (unzip 3ChannelsCMS.pcp file to any location)
    The project counts the number of Red and White dots in the parent area and reports the count, area and percentage in the output table. 
    I've also attached a video (zipped) that demonstrates how to use the app with your samples.
    If you follow all the steps shown in the video correctly, you should end up with this table:



    Regarding calibration - you must have either a reference object or know pixel size to create calibration. You can check other video tutorials on our website that show how to use Premier in details: http://www.mediacy.com/resources/media


    Regards,

    Yuri

  • edited July 2017
    CMS,

    If you want to draw the outline manually, then you don't really need the app, just use standard Premier tools:

    1. Draw polygonal ROI on Green channel.
    2. Add this ROI to the Features Manager.(Select tab, Features group)
    3. Activate Red channel.
    4. Set the ROI from the Features Manager to the Red channel.
    5. Segment and Count red spots within ROI. Data table will have all the measurements including statistics (Sum).
    6. Repeat steps 3-5 for Cy5 (white) image.

    Here is how the result may look:


    Yuri
  • Thanks yuri once gain. I will try.
    Best,
    CMS
  • 2017-07-24-091155

    CMS --

    I think that YURI has given you some very good advice.

    Another way to tackle this is to use the SMART SEGMENTATION TOOL within PREMIER.

    If your computer has the horsepower to handle a composite image, then you can tackle the your challenge as illustrated below.

    The IMAGE on the LEFT is the ORIGINAL COMPOSITE with BEST FIT DISPLAY OPTION ON.

    The IMAGE on the RIGHT is the ORIGINAL COMPOSITE with the BEST FIT DISPLAY OPTION OFF and an OVERLAY for the FEATURES found from a RED CLASS and BLUE CLASS in the SMART SEGMENTATION TOOL.

    The DATA TABLE on the UPPER RIGHT is on ALL FEATURES.

    The DATA TABLE on the LOWER RIGHT is on FEATURES PER CLASS.  Please note that PREMIER will not display two DATA TABLES like this simultaneously.  I did a SCREEN SHOT of two PREMIER SCREENS, overlaid them, and erased the appropriate sections to allow the second DATA TABLE to appear.

    Dividing the TOTAL RED AREA or the TOTAL BLUE AREA by the appropriate PER AREA will give you the GREEN AREA.

    (Yuri . . . The lower DATA TABLE illustrates an issue that I have had a difficult time documenting where COLUMN HEADINGS are not displayed sometimes).

    I hope this information is helpful.

    -- Matt

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


  • thank you Matt,

    That helps too.

    Best,

    CMS


  • Hi again,

    I made spatial calibration for my images and saved, but do I need to click on every image to activate the calibration???

     How can I integrate into the app so that by default the calibratzion added in a batch processing.

    thanks


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