H&E vs. MicroCT Comparisons

MicroCT (micro computerized tomography) is an X-ray based process where serial images are taken around an axial rotation. The method is analogous to that used for the 3D imaging of human structures, albeit on a smaller scale. It is dependent upon the interaction of large atoms with X-ray beams and requires the use of contrast agents, still in development, for imaging anything other than bone. The preliminary images are obtained from Numira Biosciences and in collaboration with Micro Photonics, Inc. (Allentown, PA). They are visualized using a comparison tool, which will allows the side-by-side comparison of multiple images and imaging modalities.

Coronal (dorsal to ventral)


Sagittal (left to right)


MicroCT X-Ray Projections

Micro CT (micron scale computed tomography) analysis of zebrafish begins with x-ray projections through the fish from 0° to 180° (mirrored to 360°) in increments of a fixed size. These x-rays are then processed using the Feldkamp algorithm to generate two-dimensional slices through the fish from any given angle. The series of aligned two-dimensional slices serves as a basis for three-dimensional reconstruction, analysis, and quantification, areas which we are actively investigating.

x-ray projection x-ray projection
Seen here are a dorsal and a ventral view of an unstained, 60 dpf juvenile zebrafish (fixed in 10% NBF). These x-ray images were generated using the SkyScan 1172 Computed Tomography System, operated and calibrated by our collaborators from Micro Photonics, Inc.