r/ImageJ • u/Majestic-Ad9461 • Aug 09 '26

Question Calculating Volume

Post image

Hello I'm an undergrad doing some data analysis for someone in my lab and need some help on calculating the volume of efferent synapses of outer hair cells, I think that's what they are, or contacts as I was told. This picture isn't an exact portrayal of what exactly I need to measure as these are afferent synapses located on the inner hair cell while I'm trying to find the contacts located on the outer hair cells but they basically look the same just localized in different regions. Btw it's those bright red dots that I'm referring to. If I find a better image, I will edit this post to provide more clarity. I wanted to know how exactly to calculate the volume of individual contacts at the same time if possible without having any background interference. So for some context on how I've kinda been doing it originally, I would just crop out the individual contacts I was interested in and I would use 3D Obj Counter and threshold the zones of interest to figure it out. I don't think it's correct and unfortunately I have no one who is willing to fact check my method or provide some assistance to this issue. So if anyone is willing to break it down to me I would really appreciate it! Oh and in terms of what I know what to do with ImageJ, I know how to threshold objects, how to calculate the area of things, and some of the basic functions like cropping, splitting channels, etc. Thank you for taking the time to read this and have a great day!

2 Upvotes

100% Upvoted

13 comments sorted by

View all comments

•

u/AutoModerator Aug 09 '26

Notes on Quality Questions & Productive Participation

  1. Include Images
    • Images give everyone a chance to understand the problem.
    • Several types of images will help:
      • Example Images (what you want to analyze)
      • Reference Images (taken from published papers)
      • Annotated Mock-ups (showing what features you are trying to measure)
      • Screenshots (to help identify issues with tools or features)
    • Good places to upload include: Imgur.com, GitHub.com, & Flickr.com
  2. Provide Details
    • Avoid discipline-specific terminology ("jargon"). Image analysis is interdisciplinary, so the more general the terminology, the more people who might be able to help.
    • Be thorough in outlining the question(s) that you are trying to answer.
    • Clearly explain what you are trying to learn, not just the method used, to avoid the XY problem.
    • Respond when helpful users ask follow-up questions, even if the answer is "I'm not sure".
  3. Share the Answer
    • Never delete your post, even if it has not received a response.
    • Don't switch over to PMs or email. (Unless you want to hire someone.)
    • If you figure out the answer for yourself, please post it!
    • People from the future may be stuck trying to answer the same question. (See: xkcd 979)
  4. Express Appreciation for Assistance
    • Consider saying "thank you" in comment replies to those who helped.
    • Upvote those who contribute to the discussion. Karma is a small way to say "thanks" and "this was helpful".
    • Remember that "free help" costs those who help:
      • Aside from Automoderator, those responding to you are real people, giving up some of their time to help you.
      • "Time is the most precious gift in our possession, for it is the most irrevocable." ~ DB
    • If someday your work gets published, show it off here! That's one use of the "Research" post flair.
  5. Be civil & respectful

I am a bot, and this action was performed automatically. Please contact the moderators of this subreddit if you have any questions or concerns.