How to count mulitple ROI in an image?

suleman

Hi,
I want to count multiple classes of cells in multiple ROI in an image,
please guide me how can i do it,
thanks,
Suleman

mbatchelor

2017-01-02-150052

Suleman --

I was away from my desk all day on FRI so I was unable to address your question as posed on 29-DEC.

If I understand your challenge, you wish to identify some areas, and then identify some features within those areas, and then classify the features within the areas, and then report measurements on the areas and the features but cluster the information PER AREA

Although I could see the EXAMPLE IMAGES you posted last week, I cannot see them now so I'll illustrate my next step to helping you with an image of of CHOCOLATE CHIP COOKIES.

It seems that you want to identify the COOKIES and then identify the CHIPS within the COOKIES and report the CHIPS (in CLASSES) and cluster the data per COOKIE.

This is illustrated in the SCREEN CAPTURE (edited to show 4 MEASUREMENT TABLES) where:

C.TIF =
Cropped and flattened version of EXAMPLE IMAGE found via GOOGLE IMAGE with manually created COOKIE AREAS 1 through 7

D.TIF =
IMAGE C with 64 CHOCOLATE CHIPS (classified as SMALL (BLUE) and LARGE (RED)) found with a SMART THRESHOLD performed on ENTIRE IMAGE

E.TIF =
IMAGE C with ROIS from COOKIE AREAS and 22 CHOCOLATE CHIPS (classified as SMALL (BLUE) and LARGE (RED)) found with a SMART THRESHOLD performed within the 7 ROIS and with

F.TIF =
IMAGE C with 3rd COOKIE AREA and 4 CHOCOLATE CHIPS (classified as SMALL (BLUE) and LARGE (RED)) found with a SMART THRESHOLD performed within the 3rd COOKIE AREA ans

I believe that you are asking the best way to get an image and data similar to F.TIF but for all of the COOKIES and all of the CHOCOLATE CHIPS that

If that is correct, I'll do my best to work out a procedure to extract this information.

I have attached a copy of C.TIF so that you can play with that image and illustrate your question better if you want.

I hope this information is helpful.

-- Matt

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

YuriG

Hi Suleman,

Please check this post http://forums.mediacy.com/discussion/comment/1520/#Comment_1520 . It shows how to count objects withing other objects and establish parent/child relations.

Yuri

mbatchelor

2016-12-29-104940

Suleman --

I have interpreted your question a bit differently then Yuri did.

I believe that you are asking about two PREMIER SKILLS that can be nested.

I have illustrated this with an image that shows 7 circles of a variety of sizes.

When the image is calibrated at 100 pix / in, the MEAN DIAMETER from PREMIER matches (almost) the stated size of the circle.

SKILL 1

Using the AUTO CLASSIFY, the 7 circles are classified by MEAN DIAMETER into two classes using images A through D.

SKILL 2

Using the MULTIPLE ROI TOOL on image E, the ROIs cause PREMIER to ignore two of the circles and then the AUTO CLASSIFY only applies to 5 circles

The ORIGINAL IMAGE (that became A.TIF) is attached as

    il_fullxfull.253764816.jpg

Please see the SCREEN CAPTURE below. 

!!! Please Note !!!
PREMIER is not capable of displaying multiple MEASUREMENT TABLE WINDOWS simultaneously.  This was achieved with a bit of PHOTOSHOPPING.

If this gives you the guidance you need, super.

If this is on the right track but you need a bit more guidance, please let me know and I'll do my best to help.

If this is off the track and your question is about something else, please let me know and I'll do my best to help.

I hope this information is helpful.

-- Matt

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

suleman

Thanks for your help Matt and Yuri,

I have more questions for Matt as this is very close to what i am trying to do:
- how do you attribute the class names to different counted circles?
- Can premier capable of counting in three ROIs made in a single image and tabulate results as classes or by ROI in the results?
I am attaching my figures showing base image where i have to count RED spots(fig1) in three different zones (which i mark by three ROI in subsequent figures from fig 2-4).
Can you tell me stepwise how to do it.

If my question is clear enough, please do reply or tell me i can rephrase my questions.
(my apology for quick screen snaps of images)

mbatchelor

Suleman --

I'll review from desk and respond later today. 

-- Matt

suleman

Thanks for all your help Matt, it was really helpful,
I really appreciate your efforts,
best regards,

Suleman