Actin Fiber Analysis using DiameterJ

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diameterj

#1

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 :slight_smile:


#2

@Dianna

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:

Hope this helps!

eta


#3


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,
Dianna


#4

@Dianna

I think @DiameterJ will be the best person to help you with your analysis using this plugin.

eta :slight_smile:


#5

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.