An organ scanned using serial section microscopy.

DIY serial section microscopy for imaging whole organs

Part of the Advanced Image and Analysis Forum. 

Many biological questions require not only high resolution imaging, but also the ability to acquire large 3D volumes of whole organs.

However, acquiring these data using conventional approaches, such as manual sectioning, is very labour intensive. Furthermore, sections on a slide will always exhibit some degree of deformation and so are difficult to reassemble into a seamless 3D volume.

Cellular level 3-D images of whole organs can be acquired using serial-section block-face microscopy, or light-sheet imaging of cleared tissue. Serial-section imaging is better suited to large samples with intrinsic fluorescence (e.g. brains containing viral-labeled neurons) since clearing of larger organs can be slow and may deform the tissue.
The presentation will describe open source hardware and software tools for the acquisition, analysis, and visualisation of 3D whole-organ imaging data. Our tools are available on the Sainsbury Wellcome Centre website.