Sample image and/or macro code
I have a field of view from calcium imaging which represents the cell bodies. I then use the coverslip from the experiment to do some stainings, including nuclei.
I am interested in locating the field of view (cell bodies) from the calcium imaging inside the larger image of nuclear stainings.
- What stops you from proceeding?
I am not able to find a package/method that could achieve what I want.
The three main problems I see are as follows:
- The problem is not looking for an exact image inside of another. I am trying to find the position of cell bodies given the nuclei.
- The histological stainings can lead to part of the cells detaching. So the template image is probably not found 100% inside the nuclei image.
- The orientation of the field of view is arbitrary. Since the coverslip is a disc, it could have been turned. So all 380° are possible.
- What have you tried already?
I tried SIFT/MOPS algorithms that come with Fiji. MOPS finds 5 similar features but when checked, they actually do not correspond.
- Have you found any related forum topics? If so, cross-link them.
- Idea for solution:
Detect cells and nuclei separately (maybe using cellpose: http://www.cellpose.org/) and then calculate the relative distances between the cell bodies. Then, use these relative distances to find the part of the nucleus image which has the highest number of correct relative distances.
I have no clue how to actually do that, it is just a though.
Other related options: https://en.wikipedia.org/wiki/PatchMatch