Help___Sprouting in fibrin gel Analysis

Safinur

Hi Guys,

I'm a novice at Image-pro and would really appreciate your help. I'm trying to analyze 100 images of HUVEC treated with drugs then sprouting in fibrin gel (see attached pic). I'm not sure where to start with this.
Thank you,
---S

YuriG

What do you want to measure?

Looking at the image, I can guess, you can measure diameter of the cell (segmenting using Smart segmentation):



Or area of the cell with all outgrowth (after Variance filter):

Yuri

Safinur

Hi Yuri!

Thank you so much for spending time to figure this out. I completely forgot to include what measures I was trying to obtain. This is a bead covered with cells, they form vessels after a couple days. I am trying to determine the length of each sprout (tube like sturcture coming out of the bead) as well as the number of sprout, and the number of branching (one tube divides in 2 or 3). ( see the example from the literature below)

Appreciate all your help Yuri!

Thank you again!

Safi


Figure from https://doi.org/10.1182/blood-2010-11-317800

mbatchelor

2018-08-16-095507

Safi --

I am not sure of the best way to tackle your challenge but here are some thoughts.

I took the last set of images that you provided and:

-- ROTATED 90 DEG COUNTER CLOCKWISE (to simplify display of results)
-- SET BRIGHT THRESHOLD

-- COUNTED OBJECTS

-- FILTERED SMALL OBJECTS AND OBJECTS TOUCHING EDGE OF IMAGE

-- MADE MASK OF OBJECTS

-- PERFORMED REDUCE FILTER TO FIND CENTER OF BEADS

-- PSEUDO COLORED TISSUE GREEN AND CENTERS RED

There is not an easy way that I know to get the distance from the CENTER to the TIPS but it can certainly be done with a MACRO that steps through the BOUNDARY POINTS and gets the DISTANCE from the BOUNDARY POINTS to the CENTER POINT.

I hope this information is helpful.

-- Matt

mbatchelor

2018-08-16-100751

Safi --

You can get in the area of the information I think you are looking for by looking at the

DIAMETER MIN

DIAMETER MAX

DIAMETER MEAN

measurements available in IMAGE-PRO.

The measurements in the image below are from the image on the far left and these DIAMETERS are not against the CENTER in the 3rd image but from the CENTROIDS of the OBJECTS in the 1st IMAGE

Here having the DATA in the DATA TABLE in ROWS is the reason I rotated your image originally so the TOP BEAD would have the TOP MEASUREMENT and the BOTTOM BEAD would have the BOTTOM MEASUREMENT.  Normally IMAGE-PRO organizes measurements by the OBJECT with the BOUNDARY POINT which is HIGHEST and FARTHEST LEFT in the IMAGE.

I hope this information is helpful.

-- Matt

Safinur

Thank you Matt!
Going to try to reproduce your example first, then attack my 100 pics....

Safi

Andrew_B

Hi Safi.  I have some ideas on how this can be done.  Please message me directly and I'd be happy to help. My e-mail address is abarlow@mediacy.com
Andrew

mbatchelor

2018-08-17-134117

Safi --

I am glad to help.

Holler with any questions.

-- Matt