I need to find edges of an arbitrary single cell image. I want to be automated otherwise I can use free hand section to determine the edges.
If all you need to do is ‘outline’ the cell - or segment it… you can simply do the following steps:
- Open your image with Bio-Formats
- Invert it
- Apply Maximum filter (radius 5 pixels)
- Apply Auto Threshold using Huang method
- Create Mask
- Analyze Particles (set size filter 100-Infinity)
Then you can save that ROI (in the ROI Manager) outlining your cell.
Here are some other helpful Segmentation links to get you started in ImageJ:
- 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 (more recently updated slides are here)
- 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 (more recently updated slides are here)
I have a single cell image not an image which has many small cells. Also I dont want to do typical analysis like counting number of cells or sizes. What I want to do is to find the border of the irregular shaped cell in my image. I can do it with free hand section of imagej but I want to be automated.
I attached one sample image to clarify what I does my shape look like. The blue line is what I want:
Please read my previous response… and check out those links. You can automate the step-wise process I laid out… via macro scripting. You should be all set now to do what you need.
Thanks for your time. I did all those steps your provided and it came nothing. I believe those steps are provided when there are several cells in an image and want to do some typical analysis.
Here is the result of the steps:
I have no idea how to do by macro scripting. Any help to start?
I did those exact steps on the example image provided - the “reference object.tif” file (hint: make sure to invert your image… you want black background)… read through all the links I provided as well. That is the best way to get you started. It’s true you might need to adapt the steps - depending on what source image you are applying them to.
Too - we recommend new users to download and use Fiji… 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.
For scripting - here are some other helpful links:
Yes I inverted the image. Would you please send the image of your output? I need something like the output of free hand not a mask. I cant do anything with a mask. I need to add those edges to the ROI.
make sure in Process > Binary > Options… that “Black Background” is selected… this can screw up mask generation with invert calls.
you have everything you need to generate your own ROIs… just try.
Sorry I am beginner in imagej cant get it. Would you please provide the steps from what I am now (I believe a mask is made) to final edge which is added to the ROI . Again: I can do it with freehand and the determined edge is added to the ROI but I do not know how to convert the mask to determined edges which are added to the ROI.
Since you are a beginner… Stop - and at minimum - take the time to go through the Segmentation workshop I linked above. Then you will feel more confident regarding the steps I provided you above. You can do it!
I checked all of those links you provided. I believe your instruction wont work in my case. If mask could detect the edge in this case why hough transform is proposed? Plus you provided the steps until the end of the masking but did not continue for other steps until added to ROI which is another reason that masking wont work here.
Thanks by the way.