I have an imaging core user who is letting me user her data set to learn ImageJ a bit more. Up until now I’ve just been playing with the images for a course I’m taking and just to see if anything I’m learning works.
I have attached two pair of images (1 and 2) with separate files for the DAPI and FITC channels of a single mitotic chromosome.
Below are her notes to me. My question and notes in bold.
An ideal work flow would be:
- crop the chromosome
Noise in the images are making it hard to threshold/segment/ROI without cropping.
Question: can we batch crop without having to do the crops manually for her 80*2 images. If so what is this plugin or tool?
threshold and segment the chromosome
I feel like I have a handle on this but because it snakes and overlaps, so I may not.
take the following measurements:
A) chromosome length (this will likely have to be manual since they are oddly shaped)
Is this true? The chromosomes are swirly and overlap. What’s the tool one uses to measure the length of something that snakes around like this?
B) chromosome area
C) background subtracted FITC intensity
I asked for clarification on this. She says she needs to do this due to camera noise but doesn’t have a camera noise only image to subtract. But if acquisition was the same throughout the whole data set (which it was), is this necessary?
D) background subtracted DAPI intensity same as C
- save to a new folder under an identifying file name not quite here yet
It would be ideal to have all of these measurements linked to the file name of the cropped chromosome so that I can refer back to if needed. I hope this makes sense, please let me know if you need any clarifications. Thanks in advance for your help!!!
I would love to figure this out with some direction on the tools to do the two things I’m stumped on - batch cropping and measuring odd-shaped lengths. Thanks in advance. -Fives