Computational protocol: Fast and precise targeting of single tumor cells in vivo by multimodal correlative microscopy

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Protocol publication

[…] The mouse brain samples were imaged in an Auriga 60 FIB-SEM instrument (Carl Zeiss Microscopy GmbH) operating under SmartSEM (Carl Zeiss Microscopy GmbH) and Atlas3D software (Fibics Incorporated, Ottowa, Ontario, Canada). The resulting datasets were aligned using TrakEM () [ImageJ ();], and the image stack was segmented in 3dmod, part of the IMOD software package () (Boulder Laboratory, University of Colorado, Denver, CO). The serial sections of the mouse ear skin tissue were screened and imaged with a Biotwin CM120 instrument (120 kV, FEI Company, Hillsboro, OR) equipped with a bottom-mounted 1 K Keen View CCD camera (Olympus Soft Imaging Solutions, Münster, Germany). Montaged images and tomograms were acquired with a Tecnai F30 Field Emission Gun TEM (300 kV, FEI Company) equipped with an Eagle 4 K camera (FEI Company). The F30 was controlled using Tecnai User Interface (PEOUI) and Tecnai Acquisition (TIA) software. Tomograms and image montages were obtained using SerialEM software (), and the tomograms were reconstructed in eTomo, part of the IMOD software package () (Boulder Laboratory). The electron microscopy images were processed using ImageJ () and Photoshop CS6 (Adobe). The figures were created in Illustrator CS6 (Adobe), and the supplementary material movies were made with Fiji (ImageJ), IMOD (Boulder Laboratory) and Amira (FEI Company). […]

Pipeline specifications

Software tools ImageJ, IMOD, SerialEM
Applications cryo-EM, Microscopic phenotype analysis
Organisms Dipturus trachyderma
Diseases Neoplasms