Ultrastructural Visualization of 3D Chromatin Folding Using Serial Block-Face Scanning Electron Microscopy and In Situ Hybridization (3D-EMISH)
Manuscript is currently available at https://www.biorxiv.org/content/10.1101/2020.02.05.935106v1
Authors: Paweł Trzaskoma1,8, Błażej Ruszczycki1,8, Byoungkoo Lee2,8, Katarzyna K. Pels1, Katarzyna Krawczyk1, Grzegorz Bokota3, Andrzej A. Szczepankiewicz1, Jesse Aaron4, Agnieszka Walczak1,5, Małgorzata A. Śliwińska1, Adriana Magalska1, Michal Kadlof3, Artur Wolny1, Zofia Parteka3, Sebastian Arabasz6, Magdalena Kiss-Arabasz6, Dariusz Plewczynski3,7, Yijun Ruan2*, Grzegorz M. Wilczyński1*
1 Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland 2 The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA 3 Center of New Technologies, University of Warsaw, Warsaw, Poland 4 Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA 5 Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznan, Poland 6 Łukasiewicz Research NETWORK – PORT Polish Center for Technology Development, Wrocław, Poland 7 Mathematics and Information Science, Warsaw Technical University, Warsaw, Poland 8 equal contribution as co-first authors
- corresponding authors: Grzegorz M. Wilczyński (g.wilczynski@nencki.gov.pl), Yijun Ruan (Yijun.Ruan@jax.org)
3D-EMISH data folders:
[Example image files] Three example 3D-EMISH images to show intermediate image processing steps
[Exemplary input] Exemplary 3D stack to perform denoising [.tif], and denoised image [.cmap] for analysis and segmentation
[Exemplary output- denoising] Exemplary output from running denoising script
[Exemplary output- analysis] Example of aligned and segmented structure
[Collected 3D-EMISH raw image files] All 229 cropped raw EM image stacks
[Code Version 1.1] 3D-EMISH image processing and analyzing codes
Instruction how to run the code are in the readme.txt file in code version 1.1 folder