Open Serial Section

Serial Section Imaging

Serial section imaging is the process of alternately imaging and slicing a block of tissue in order to obtain a 3D volume. There are many variants of this approach, ranging from EM to light microscopy. This site concentrates on block-face serial section 2-photon imaging of brain tissue, however the tools we present here can be used for other organs and other imaging systems (e.g. confocal, widefield, knife-edge imaging, etc).

Our Tools

This site presents open source tools used at the Sainsbury Wellcome Centre (UCL) for acquisition, analysis, and visualisation of serial section imaging data. We make available both published and unpublished software via our Serial2P GitHub team. The main highlights are:

• BakingTray acquisition software
• StitchIt, our tile-stitcher for MATLAB.
• cellfinder for automatic cell counting

• BrainRender for 3-D visualisation

• Our blog contains a variety of information and is organised by date, by tag, or by category.