I do not know what your MICROGRAPH IMAGES look like so I've done a bit of PROTOTYPING using one of my favorite examples, CHOCOLATE CHIP COOKIES.
In the screen capture below:
A = ORIGINAL IMAGE B = MONO version of A C = INVERSE of B D = ENHANCED version of C with 9 OBJECTS (using MANUAL THRESHOLD + MANUAL SPLITTING and MANUAL DELETES) E = ROIS created from OBJECTS in C (using FEATURE MANAGER) on PIXELS from C F = E + OBJECTS from DOUBLE MANUAL THRESHOLD inside ROIS seen in E
The two MEASUREMENT TABLES (that are PHOTOSHOPPED to appear simultaneously) are for IMAGES D (LEFT) and F (RIGHT).
The 9 ROIS from D (and E F) can be handled individually if that suits the needs of your work better.
I hope this information is helpful but if you can supply an example image, I can probably do a better job of assisting you.
Please see the SCREEN CAPTURE below that illustrates one of the ways that you could move from your ORIGINAL IMAGE through to a measure of the WHITE SPACE in the TISSUE.
In the SCREEN CAPTURE please see:
ORIGINAL IMAGE = 838 2 20x.tif calibrated according to CALIBRATION BAR (0.3755 um/pix) A = CROP of ORIGINAL IMAGE to avoid issues with CALIBRATION BAR and EDGES B = MASK of DARK OBJECTS (set automatically) in A C = CROP of ORIGINAL IMAGE to avoid issues with CALIBRATION BAR and EDGES D = MASK of BRIGHT OBJECTS (set manually) in C MEASUREMENT TABLES for B (TISSUE) and C (WHITE SPACE)* EXCEL TABLE with B and C DATA and calculation of TOTAL C AREA / TOTAL B AREA
There are other ways to tackle this challenge but hopefully this will illustrate one that generate the results you need.
The process illustrated above could be automated with a PREMIER MACRO PROJECT.
I hope this information is helpful.
-- Matt
* MEASUREMENT TABLES for each image are shown individually by PREMIER. Both appear simultaneously in this SCREEN CAPTURE thanks to PHOTOSHOP.
Hi, I have a similar naive question. I have a Trichrome stained image in which I wanted to measure blue area in the subepithelial region (ROI in yellow circle) of the airways only and compare with different groups. Major problem is intensity of blue area varies from very-2 light blue to dark blue. And also the the bronchioles varies in area from small to very large. So how to measure it. attached 2 different image for your ref. Thanks for your kind help.
I believe that you would like to measure the BLUE STAINED AREA within the ROI.
Your image was difficult to work on because the YELLOW ANNOTATION / ROI was confounding things. I found a similar image on the INTERNET and then worked through a process that I believe will provide the information you need.
Please see the SCREEN CAPTURE below that illustrates moving from:
A = ORIGINAL IMAGE B = ORIGINAL IMAGE with CONCENTRIC ROIS C = CROP of B C MASK = SMART THRESHOLD MASK of C D = CROP of B D MASK = BRIGHT THRESHOLD MASK of D
C MASK and D MASK can be measured to generate BLUE STAINED AREA and ROI AREA.
You can also get ROI AREA by measuring AREA and PERCENT AREA in C MASK and then back figuring the ROI AREA.
Thanks Beth for your illustration. I am trying to use your script in my software if I can able to do that analysis with different images. I am afraid I didnt receive your mail. my email is amehta@lji.org in case.
Comments
Yuri
I do not know what your MICROGRAPH IMAGES look like so I've done a bit of PROTOTYPING using one of my favorite examples, CHOCOLATE CHIP COOKIES.
In the screen capture below:
A = ORIGINAL IMAGE
B = MONO version of A
C = INVERSE of B
D = ENHANCED version of C with 9 OBJECTS (using MANUAL THRESHOLD + MANUAL SPLITTING and MANUAL DELETES)
E = ROIS created from OBJECTS in C (using FEATURE MANAGER) on PIXELS from C
F = E + OBJECTS from DOUBLE MANUAL THRESHOLD inside ROIS seen in E
The two MEASUREMENT TABLES (that are PHOTOSHOPPED to appear simultaneously) are for IMAGES D (LEFT) and F (RIGHT).
The 9 ROIS from D (and E F) can be handled individually if that suits the needs of your work better.
I hope this information is helpful but if you can supply an example image, I can probably do a better job of assisting you.
Good luck.
-- Matt
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
This is an H&E stain, and I need to do a quantitative analysis of the white space between the cells
-- Matt
Beth
I received the EXAMPLE IMAGE that you sent.
Please see the SCREEN CAPTURE below that illustrates one of the ways that you could move from your ORIGINAL IMAGE through to a measure of the WHITE SPACE in the TISSUE.
In the SCREEN CAPTURE please see:
ORIGINAL IMAGE = 838 2 20x.tif calibrated according to CALIBRATION BAR (0.3755 um/pix)
A = CROP of ORIGINAL IMAGE to avoid issues with CALIBRATION BAR and EDGES
B = MASK of DARK OBJECTS (set automatically) in A
C = CROP of ORIGINAL IMAGE to avoid issues with CALIBRATION BAR and EDGES
D = MASK of BRIGHT OBJECTS (set manually) in C
MEASUREMENT TABLES for B (TISSUE) and C (WHITE SPACE)*
EXCEL TABLE with B and C DATA and calculation of TOTAL C AREA / TOTAL B AREA
There are other ways to tackle this challenge but hopefully this will illustrate one that generate the results you need.
The process illustrated above could be automated with a PREMIER MACRO PROJECT.
I hope this information is helpful.
-- Matt
* MEASUREMENT TABLES for each image are shown individually by PREMIER. Both appear simultaneously in this SCREEN CAPTURE thanks to PHOTOSHOP.
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
amehta17 --
I believe I understand your challenge.
I believe that you would like to measure the BLUE STAINED AREA within the ROI.
Your image was difficult to work on because the YELLOW ANNOTATION / ROI was confounding things. I found a similar image on the INTERNET and then worked through a process that I believe will provide the information you need.
Please see the SCREEN CAPTURE below that illustrates moving from:
A = ORIGINAL IMAGE
B = ORIGINAL IMAGE with CONCENTRIC ROIS
C = CROP of B
C MASK = SMART THRESHOLD MASK of C
D = CROP of B
D MASK = BRIGHT THRESHOLD MASK of D
C MASK and D MASK can be measured to generate BLUE STAINED AREA and ROI AREA.
You can also get ROI AREA by measuring AREA and PERCENT AREA in C MASK and then back figuring the ROI AREA.
I hope this information helps.
-- Matt
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-
Thanks again
A