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I have been working on yeast cells to analyse the effect of DNA damaging agents on mitochondrial structure. I have imaged my culture treated with MMS for a period of 6 hours and while observing the images, I suspect there is fragmentation of mitochondria in later point of time. So, I am wondering if I can get measurements of mitochondria using z stack images.

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    $\begingroup$ Welcome to Biology.SE! Can you expand on your protocol (both to encourage answers and to make it easier for other non-experts to understand both the question and the answer)? We have been doing some z-stack imaging for a separate project (imaging viral dissemination in insect tissues) but there isn't enough in your question yet for me to tell exactly where you're having problems. $\endgroup$
    – arboviral
    Commented Mar 25, 2018 at 14:26
  • $\begingroup$ Sorry for providing insufficient information. I have stained yeast cells with mito tracker dye (for mitochondrial staining) and analysed samples for 6 hours, by taking out 1 ml of culture at every one hour. While imaging culture, I captured z stack images for these 7 time points (starting from zero hour). Now, I have been looking for applications that can provide me the measurements (dimensions) of stained mitochondria using Z stacked images. $\endgroup$ Commented Mar 25, 2018 at 14:46

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ImageJ is usually the standard software to measure cell characteristics, a little bit of a learning curve but there is a large suite of analysis methods and image adjustments/filters.

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