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,