ImageJ - Part 2: Object Analysis

You can use ImageJ to extract color information, and look at specific parts of an image. In this video, we look at HeLa cells, which are derived from an old cell line obtained (without permission) from Henrietta Lacks. These cells are cancerous and also considered to be immortal. More information about these cells is available on the wikipedia page. The goal of this tutorial is to show how to determine the area of these four nuclei, as well as some other shape descriptors. The corresponding activity can be found at www.mlkstemacademy.blogspot.com

[@wolominok]

Friendly and useful, thanks a lot.

[@baxter0425]

This was a quick tutorial I put together for my engineering class. Not too many details shown here. But yes You can also figure out the diameter, very easily. You would use a characteristic called ECD or equivalent circular diameter. Assuming that the object is not a string or something with a length/width ratio that is too large. When you click on shape descriptors as part of step 6, the ECD value is automatically calculated and refers to the diameter of the object.

[@ryanbaxter4248]

Hey Pierre, You certainly can. You would segment the shape in question for each slice. Essentially, trace the item in question. Then you can follow the tutorial for creating an object out of the traced region. This region would need to be assigned its own color. If there are not too many and there is a set of identifiable features, this could be performed in batch using a macro. Couldn't say without seeing the images. Then you can add the images together, Original + segmented, and merge the image and save as a new filename. After each slice is completed, you could restack the images. You may have to play with the opacity/transparency of each layer but this would give you a stack of images with the object in color and 3D. If you send me an example image, I could give you more specific instructions.

[@Abdullblo]

hi there
i am inserted in counting muscle fiber any ideas how to do that?
many thanks

[@dr.muhammadasif2368]

Hello everybody. I have stained HCT 116 cells with Hoechst and Rhodamine fluorescent dyes now I want to quantify number of apoptotic cells/field. Please let me know if there is any way to do this using ImageJ.

[@DarthVirtus]

Is there a way to measure the diameter of particles using ImageJ?

[@baxter0425]

Sorry...I just rewatched my video and the last step was missing. Using the area value, you can calculate ECD by following this formula: ECD = 2*sqrt(Area/pi).