Measurement of capillary diameter

[Henri_Pioneer]

Sample image and/or code

• Upload an original image file here directly or share via a link to a file-sharing site (such as Dropbox) – (make sure however that you are allowed to share the image data publicly under the conditions of this forum).
• Share a minimal working example of your macro code.

Background

• What is the image about? Provide some background and/or a description of the image. Try to avoid field-specific “jargon”.

This is the pericyte cells (red) and vessels (green).

Analysis goals

• What information are you interested in getting from this image?
  I want to get diameter of vessels.

Challenges

• What stops you from proceeding?
  segmentation and diameter measurement.

• What have you tried already?
  I tried segmentation of vessels using Image J and Icy.

• Have you found any related forum topics? If so, cross-link them.
  No

• What software packages and/or plugins have you tried?

I tried Image J and Icy.

[Research_Associate (MicroscopyRA)]

Might want to look into some topics like these for FIJI.

Automatic Length and Width Measurement of Threholded ROI

The Bounding rectangle option in Analyze > Set Measurements… might be what you need.

Measuring thickness (or width) of cracks

Another way could be to used the product of the Distance Map and the Skeleton of the thresholded binary image. The result is the distance to the outer contour for each of the skeleton points (which are the maxima of the distance map and therefor a kind of major axis of the crack). The following macro applied to the posted image should demonstrate the principle: setOption("BlackBackground", true); setThreshold(69, 132); run("Convert to Mask"); rename("orig"); run("Duplicate...", "title=dis…

[Henri_Pioneer]

@Automatic Length and Width Measurement of Threholded ROI

Bounding rectangle option

Thank you very much. “Bounding rectangle option” is good for me. But I have multiple capillaries need to measure. But it seems just appear mean value of it. How can I get individual value of width and height?

[Research_Associate (MicroscopyRA)]

Not sure, you should be getting one line per ROI.

[Henri_Pioneer]

I segmented below image using Weka. After that, how can I get each ROI like your picture? I am a beginner, sorry to ask this kind of question.

[Henri_Pioneer]

I figure out. Thank you very much!

[Mathew]

@Henri_Pioneer
The information you are looking for will probably be there:

Trainable Weka Segmentation

Good reading

[Henri_Pioneer]

Yes, it is! When I finished reading all the sentences! Thank you very much.