Hi, I am trying to use Diameter J to analyze actin fibril diameters in fluorescent microscopy. I have tried image types .gif .tif and .jpeg and get error messages every time. I can’t get the image segmented, and am wondering if I have the wrong format? I do not have access to raw images as I am analyzing data collected last year, and used photoshop to convert to RGB color. I am new to this program and hope someone can help! Thank you
Welcome to the Forum and ImageJ in general.
I haven’t used DiameterJ much myself… so perhaps others here have better insight on that particular plugin - but we can at least get the ball rolling…
What are the types of images you are working with? You mentioned .gif, .tif, and .jpeg (warning: DO NOT USE JPEG for quantification analyses… this is why) - so are you converting the original images each time? Would you be able to attach the most raw/original image files you have? At least one for an example for us to test.
You can convert images to RGB in ImageJ (whatever processing you do to your images - keep it all in ImageJ if you can - to keep it more reproducible, etc) - you can search the ImageJ User Guide. Here are a few other helpful links for getting started with ImageJ/Fiji:
- ImageJ wiki - the best place to learn everything about ImageJ/Fiji!!
- “Introduction to Fiji” workshop and corresponding slides- worth the time to get a solid intro
- Principles page - collection of principles for the entire image analysis process, from acquisition to processing to analysis
- Segmentation page
“Segmentation in Fiji” workshop and corresponding slides
NOTE: Fiji is Just ImageJ - it is simply a distribution of ImageJ that comes with a bunch of plugins bundled - ready for you to use out-of-the-box. If you are just getting started, we recommend downloading/using Fiji.
Hope this helps!
This is one of the images, it is the most raw version I have access to. What I have been doing so far is downloading this type of image, then converting to RGB color and then trying to put it back into the DiameterJ program. I am open to any suggestions to analyze my images or on the process I’ve been using.
Thank you very much for your help,
I think @DiameterJ will be the best person to help you with your analysis using this plugin.
Hello all and sorry for being late to the discussion. In general DiameterJ is meant to analyze grey-scale 8-bit or 16-bit images, not RGB. So that might be the problem. However, I would encourage you to take the DiameterJ training. It is the easiest way to learn to use DiameterJ (and how to process your iamges) it is free a free online training tool at https://sites.google.com/site/diameterj/ . If you have any questions after that. Please let me know.