The Laboratory of biological electron microscopy and structural biology

(dr. fei sun’s lab)

 
 

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Large scale, high resolution three dimensional (3D) ultrastructural reconstruction of cells and tissues has become increasingly important to our understanding of complex biological systems. There have been a few partial 3D ultra-structures of Caenorhabditis elegans (C. elegans) reported, however 3D reconstruction of a whole nematode has never been achieved. Here, we independently developed a technique called automatic collector of ultrathin sections scanning electron microscopy and using this methodology, generated a 3D reconstruction of an entire C. elegans larva with 100 nm axial and 15 nm lateral resolution. Compared to the current available ATUM (automated tape-collecting ultramicrotome) technique, our work provides another alternative complete solution that can be applied to obtain large scale 3D ultrastructure of tissues. Our workflow includes an automated hardware system for high throughput serial section collection, a software package for automatic SEM imaging, and an image reconstruction program. These combined techniques can now be used together to rapidly provide access to understand the anatomy of the whole nematodes.



Reference:

Li X., Ji G.*, Chen X., Ding W., Sun L., Xu W., Han H., and  Sun F.* (2017), Large scale three-dimensional reconstruction of an entire Caenorhabditis elegans larva using AutoCUTS-SEM. Journal of Structural Biology, 200(2): 87-96. doi: 10.1016/j.jsb.2017.09.010. (The package for automatic SEM data collection can be downloaded from here.)


The database of scanning electorn microscopy of serial sections of a whole C.elegnas larva

The original unprocessed data can be obtained here (size: 6.2Gb).

The aligned processed data can be obtained here (size: 661Mb).

The tiff stack of original data with four fold compression can be obtained here (size: 1.2Gb).

The tiff stack of aligned data with four fold compression can be obtained here (size: 1.1Gb).

Large scale three-dimensional reconstruction of an entire Caenorhabditis elegans larva using AutoCUTS-SEM

AutoCUTS device (a) and one slice of reconstructed larva architecture (b).

(In collaboration with Center for Biological Imaging, Institute of Biophysics, CAS)