Segment mitochondria using Trainable Weka Segmentation

Dear All,

I am trying to segment this image using trainable weka segmentation. The previous posts were so helpful in understanding the process. I kindly request an expert advice on this image, how to segment out mitochondria from the rest. The goal is to calculate the surface area of the mitochondria. Kindly advice.
Thank youPicture1a.tif (179.7 KB)


As far as how to use Trainable Weka… check out the ImageJ wiki page on the plugin:

You can also go through the section of the Segmentation workshop that covers how to get started using the plugin (also linked in the thread you referenced - along with slides).

But to start - the most important thing is the quality of data with which you are working. Your image is quite low resolution… do you have higher resolution images? That will make everything easier - and more reliable and reproducible - down-the-analysis-road.

Hi Ellen T Arena,

I thank you for the comment.I am looking for weka segmentation of EM images. I tried the wiki plugin help. The issue I am facing is the segmentation doesn’t separate mitochondrion from background.

If you have this expertise, Would it be possible for you to guide me with one image?

Thank you,


There are tons of folks here that can help - in addition to me. But let’s start with the last question I asked you in my previous post:

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