Intestinal villi measurement

Hello, Im currently working on my thesis, which consist on the measurement of intestinal villi on broilers after they consumed a probiotic mixture but they supposed to be immune compromise, due their mothers are old breeder hens. I’m being trying different examples, closing eyes here and there, but I can’t make the measurement, the software still open a lot of windows but I just need for the moment the area, width and height. I tried to manually select the villi to be measured but I couldnt. I used the only example of pipelines about vessels and villi that I found but I don’t need second objects for now, is all really confusing for me now, so after being familiar with the software for a while I decided ask for help. I definitely know, I’m doing something wrong but I just cant figure out for know what it is. I will like to measurement crypts deep to, so I will like to know if is some manual tool that can help me with that too. Im attaching and example of the images I’m using with this purpose.

I will really appreciate your help.


Catherine Gutierrez
Veterinary Medicine Student
Facultad de Ciencias Agropecuarias
Programa de Medicina Veterinaria
Universidad de La Salle
Bogota, Colombia


This pipeline will hopefully get you started. Stained tissue slides are actually much harder than fluorescent images to quantify, so as you mentioned a manual approach, that is the simple attempt I made here.

(1) UnMixColors is an attempt at least to get grayscale intensity values from your color histological samples. I chose Eosin, but that was just a guess. Please choose yourself to deconvolve the colors that best matches your stain.
(2) IdentifyObjectsManually some functionality to draw on the image to define objects. If you want to define villi or crypts automatically, that is a much harder problem than you might think! I would stick with the manual solution unless you really need to do this in high throughput (if so, you’d need to annotate these structures for us, since we are not intestinal experts! :smile: )
(3) MeasureObjectSizeShape will measure various features of each object segmented.
(4) Export* – it looks like it is complaining but you simply need to define an output folder here on your local machine.

Let us know if this helps,
DL_Manual.cppipe (5.03 KB)