Array tomography: characterizing FAC-sorted populations of zebrafish immune cells by their 3D ultrastructure

For 3D reconstructions of whole immune cells from zebrafish, isolated from adult animals by FAC-sorting we employed array tomography on hundreds of serial sections deposited on silicon wafers. Image stacks were either recorded manually or automatically with the newly released ZEISS Atlas 5 Array Tomography platform on a Zeiss FEGSEM. To characterize different populations of immune cells, organelle inventories were created by segmenting individual cells. In addition, arrays were used for quantification of cell populations with respect to the various cell types they contained. The detection of immunological synapses in cocultures of cell populations from thymus or WKM with cancer cells helped to identify the cytotoxic nature of these cells. Our results demonstrate the practicality and benefit of AT for high-throughput ultrastructural imaging of substantial volumes. LAY DESCRIPTION: To look at immune cells from zebrafish we employed array tomography, a technique where arrays of serial sections deposited on solid substrates are used for imaging. Cell populations were isolated from the different organs of zebrafish involved in haematopoiesis, the production of blood cells. They were chemically fixed and centrifuged to concentrate them in a pellet that was then dehydrated and embedded in resin. Using a custom-built handling device it was possible to place hundreds of serial sections on silicon wafers as well ordered arrays. To image a whole cell at a resolution that would allow identifying all the organelles (i.e. compartments surrounded by membranes) inside the cell, stacks of usually 50–100 images were recorded in a scanning electron microscope (SEM). This recording was either done manually or automatically using the newly released Atlas Array Tomography platform on a ZEISS SEM. For the imaging of the sections a pixel size of about 5 nm was chosen, which defines membrane boundaries very well and allows segmentation of the membrane topology. After alignment of the images, cellular components were segmented to locate the individual organelles within the 3D reconstruction of the whole cell and also to create an inventory of organelles. Based on their morphologies we could identify specific cell types in the different hematopoietic organs. We could also quantify the proportion of each cell type in the whole population isolated from a given organ. Some of these specific cells from zebrafish were grown in a culture dish together with human cancer cells. By time-lapse light microscopy we observed that the fish cells attacked the cancer cells and killed them. From this we concluded that these cells must be similar to the cytotoxic cells from humans that play an important role in defence against spontaneously arising cancer cells in our bodies. They form special structures, called immunological synapses that we could also identify on our arrays and reconstruct in 3D. This is the first time the potential of zebrafish immune cells to form immunological synapses has been demonstrated. Our study is a good example for the practicality and benefit of array tomography in high-throughput ultrastructure imaging of substantial volumes, applicable to many areas of cell and developmental biology.