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A large-scale heterogeneous unlabeled cellular electron microscopy image dataset for deep learning methods.

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Enforcing prediction consistency across orthogonal planes significantly improves segmentation of FIB-SEM image volumes by 2D neural networks.

Ryan W Conrad Hanbin Lee and Kedar Narayan


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Efficient skeleton editing in a VR environment facilitates accurate modeling of highly branched mitochondria

Ryan W Conrad, Thomas Ruth, Falko Löffler, Steffen Hadlak, Sebastian Konrad, Christian Götze, Christopher Zugates, Molly McQuilken and Kedar Narayan


Towards Artifact-free FIB-SEM datasets: Strategies during image acquisition of resin-embedded biological samples

Kedar Narayan, Alexandre Laquerre and Michael Phaneuf


Super-resolution cryo-fluorescence microscopy of high-pressure-frozen thick samples: a screening study of C. elegans

Irene Y Chang, Mohammad M Rahman, Adam Harned, Orna Cohen-Fix and Kedar Narayan

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Cryo LM of high-pressure-frozen thick samples (C. elegans)

This video describes a workflow to execute cryo fluorescence microscopy on high-pressure-frozen C. elegans worms. This collaboration with Carl Zeiss GmbH was presented (Poster #1085) at Microscopy & Microanalysis 2020.

“2.5D” Neural Network based segmentation of mitochondria

This video describes a method to enforce prediction consistency across orthogonal planes (hence 2.5D) to improve neural network segmentation of mitochondria in a FIB-SEM image volume. This work was presented (poster #831) at Microscopy & MIcroanalysis 2020.

Towards artifact-free FIB-SEM acquisition

This video describes artifact-free FIB-SEM data acquisition strategies, and accompanied a poster (#535) presented at Microscopy & Microanalysis 2020

Editing mitochondrial skeletons in a virtual reality (VR) environment

In this movie, we describe a module in ArivisVR to import, edit and export corrected mitochondrial skeletons. This work (in collaboration with arivis Inc) was presented (Poster #448) at Microscopy & Microanalysis 2020.

Non-CMM Publications of Interest

Volume microscopy in biology: FIB-SEM tomography.

Kizilyaprak C, Stierhof YD, Humbel BM. Tissue Cell. 2019 Apr;57:123-128

PubMed Link

Enhanced FIB-SEM systems for large-volume 3-D imaging.

Xu CS, Hayworth KJ, Lu Z, Grob P, Hassan AM, García-Cerdán JG, Niyogi KK, Nogales E, Weinberg RJ, Hess HF. Elife. 2017 May 13;6.

PubMed Link

Minimal resin embedding of multicellular specimens for targeted FIB-SEM imaging.

Schieber NL, Machado P, Markert SM, Stigloher C, Schwab Y, Steyer AM. Methods Cell Biol. 2017;140:69-83.

PubMed Link

Exploring the third dimension: volume electron microscopy comes of age.

Peddie CJ, Collinson LM. Micron. 2014 Jun;61:9-19.

PubMed Link

Correlative 3D imaging of whole mammalian cells with light and electron microscopy.

Murphy GE, Narayan K, Lowekamp BC, Hartnell LM, Heymann JAW, Fu J and Subramaniam S. J Struct Biol. 2011 Dec;176(3):268-78.

PubMed Link

Three-dimensional imaging of HIV-1 virological synapses reveals membrane architectures involved in virus transmission.

Do T, Murphy G, Earl LA, Del Prete GQ, Grandinetti G, Li G, Estes J, Rao P, Trubey C, Thomas J, Spector J, Bliss D, Nath A, Lifson JD, and Subramaniam S. J Virol. 2014 Sep;88(18):10327-39.

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Multi-resolution correlative focused ion beam scanning electron microscopy: applications to cell biology.

Narayan K, Danielson CM, Lagarec K, Lowekamp BC, Coffman P, Laquerre A, Phaneuf MW, Hope TJ, and Subramaniam S. J Struct Biol. 2014 Mar;185(3):278-84.

PubMed Link