Hi all, I have a very specific need, which I haven’t managed to solve (for distinct reasons) with available software. The data that I have is composed of 2D images (8bit single channel (DAPI) .tif files) of brain slices (each image is one full coronal mouse brain slice). Using a custom pipeline I find cells of interest (using the other channels on that image that for the current purpose is not important) and annotate their 2D coordinates (relative to each particular image). So what I have is a set of 2D images and points of interest (image_id, x_position, y_position.
The aim is to add this information (the coordinates of the cells of interest) to the 3D brain atlas (the Allen Institute one), so that I can combine the information for different slices and different mice (sliced with different angles, and the slices are not matching 100% in between mice either). The end result would be, for each point of interest, its position in the 3D atlas (x_position, y_position, z_position).
My initial thought was to find a transformation, using elastix, directly from the 2D slice to the 3D atlas, but I don’t think that is possible atm.
My plan now is to find, for each physical brain slice that I have, the corresponding slice in the atlas (using big data viewer, or any available matlab plugin designed for this, that doesn’t matter), and then calculate the 2D-2D transformation using elastix (probably a non-rigid one). Then, apply that transformation to the coordinates of the cells of interest, and then ‘put those coordinates’ into the 3D volume. For that I would need to use the information of the 3D position of my virtual slice.
Is there any software that allows this?
In a nutshell what I need is: slice a 3D volume in any orientation and save two things:
- the virtual slice as a .tif image.
- for every pixel in the virtual slice (1), the corresponding xyz positions of the atlas (this could be used as a look up table). Alternatively, a transformation that can be applied to a 2D point to get a 3D point.
Any help is much appreciated