Workflow advice for 3d reconstruction of histological slices

[Kevin92 (Kevin)]

Hi everyone,

I’ve started a project aiming to generate 3d models out of histological embryological slices.

Here are some examples of the images:

I’m new to image processing and have been working with Fiji but I’m having some difficulties.

I’m looking for some advice regarding my workflow.

1. Registration - I’ve been working with TrakEM2 using manual/automatic alignment with some success.
2. Different intensities/ stains etc - I’m unsure as to approach this. Note how the different slides have different intensities of staining.
3. Segmentation - I want to segment structures such as the intestines and the abdominal cavity. Ideally I’d like to use something like WEKA however I’m unsure how feasible that would be for these images.
4. 3D reconstruction

Many Thanks

[susan-sheehan]

I did something similar with kidney’s I used Stack registration to do the alignment of multiple sections. I had Images stained differently than you do. I did my 3D reconstructions in Imaris and then was able to use their volume tool to segment and get counts.