3d Projection Light sheet


I’m trying to do a 3D reconstruction using a image stack that acquired from a light sheet scope using the 2X objective.
For some reasons It looks really nice when you check in the z projection, but they dont look nice in 3D. I’m trying to use different software to see if I can improve the quality of the 3D projection, but I’m not sure how to start or if I need any specific scrip. I have access to Imaris and Image J.

Can you post a screen shot of the projection and the 3D view?? Then it may be easier to see what is happening and for people to help you.

The green color looks ok, but the red color in the z proyection looks good but in 3D proyection really bad.

Thanks for posting @CARLOS_LIZAMA. Unfortunately I don’t have detailed knowledge regarding the 3D Visualization plugins, and am unsure how to advise you. At first glance it looks like the green channel is more transparent, thus you can see details in the middle of the specimen better. Hopefully those who are more knowledgable about the visualization rendering options will be able to give you some tips.