I do believe this method is working, but I just have a feeling that something is still off about what I’m doing, plus there is very little consistency between images. Then Ctrl+M to get the %Area of what is within the ROI. And then I click add to place it into the ROI manager. Add threshold using more arbitrary numbers (33 for the top bar and 255 for the bottom). Subtract background (reducing to an arbitrary number for each image (50) which I have seen to show a lot of inconsistency and I hate this method). Close all of the windows except for the split channel that is labeled as “green”, which is actually grayscaled. I want to threshold the entire image but be able to adjust is accordingly so I can get a good representation of a percentage that is within the ROI. Here, you can see the original images plus my attempt at quantifying the percentage of thresholded amount of color within the ROI that I have drawn. “Segmentation in Fiji” workshop and corresponding slides.Principles page - collection of principles for the entire image analysis process, from acquisition to processing to analysis.“Introduction to Fiji” workshop - worth the time to get a solid intro. ImageJ wiki - the best place to learn everything about ImageJ/Fiji!!.Here are some other super helpful links to get you started with ImageJ, Image Analysis, and Segmentation: Would you be able to post an image that show what you want to measure exactly? How are you setting your thresholds at the moment - what is your current workflow?Īlso - do you have other channels to define the ROI and then measure your nephrin staining? In general - it is never really a good idea to use the signal you want to measure the intensity of to set the threshold for your ROIs… Check out this older Forum post that explains this issue with measurements of intensity involving a threshold on the same channel as the one being measured. So… let’s see about getting you some help. To the Forum and the wonderful world of ImageJ!
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |