BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples.

Nature Methods
David HörlStephan Preibisch

Abstract

Light-sheet imaging of cleared and expanded samples creates terabyte-sized datasets that consist of many unaligned three-dimensional image tiles, which must be reconstructed before analysis. We developed the BigStitcher software to address this challenge. BigStitcher enables interactive visualization, fast and precise alignment, spatially resolved quality estimation, real-time fusion and deconvolution of dual-illumination, multitile, multiview datasets. The software also compensates for optical effects, thereby improving accuracy and enabling subsequent biological analysis.

References

Jul 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Barret D PfeifferGerald M Rubin
Feb 7, 2009·Journal of Microscopy·M EmmenlauerH Burkhardt
Apr 7, 2009·Bioinformatics·Stephan PreibischPavel Tomancak
May 29, 2010·Nature Methods·Stephan PreibischPavel Tomancak
Jun 2, 2010·The Journal of Cell Biology·Melissa LinkertJason R Swedlow
Jun 13, 2012·Nature Methods·Stephan SaalfeldPavel Tomancak
Jun 30, 2012·Nature Methods·Johannes SchindelinAlbert Cardona
Sep 11, 2012·Bioinformatics·Tobias PietzschStephan Saalfeld
Nov 28, 2012·BMC Bioinformatics·Alessandro Bria, Giulio Iannello
Apr 12, 2013·Nature·Kwanghun ChungKarl Deisseroth
Apr 30, 2013·Nature Methods·Robert P J NieuwenhuizenBernd Rieger
Apr 22, 2014·Nature Methods·Stephan PreibischPavel Tomancak
Jun 20, 2014·Nature Protocols·Raju TomerKarl Deisseroth
Jan 17, 2015·Science·Fei ChenEdward S Boyden
May 27, 2015·The Journal of Cell Biology·Carlas S SmithDavid Grunwald
May 29, 2015·Nature Methods·Tobias PietzschPavel Tomancak
Jul 18, 2015·Cell·Douglas S Richardson, Jeff W Lichtman
Oct 27, 2015·Nature Methods·Raghav K ChhetriPhilipp J Keller
Dec 3, 2015·Bioinformatics·Christopher SchmiedPavel Tomancak
Jul 16, 2016·WormBook : the Online Review of C. Elegans Biology·Xantha Karp
Nov 1, 2016·Nature Biotechnology·Loïc A RoyerPhilipp J Keller
Apr 7, 2017·Bioinformatics·Corinna BlasseEugene W Myers
May 26, 2017·PLoS Computational Biology·Jeffrey P NguyenAndrew M Leifer
Sep 22, 2017·Nature Communications·Duncan P RyanDouglas P Shepherd
Apr 14, 2018·PLoS Computational Biology·Martin WeigertMoritz Kreysing

❮ Previous
Next ❯

Citations

Jan 4, 2020·Nature Reviews. Neuroscience·Hiroki R UedaPhilipp J Keller
Sep 29, 2019·Nature Methods·Venkatakaushik VoletiElizabeth M C Hillman
Sep 19, 2019·Nature Methods·Fabian F VoigtFritjof Helmchen
Nov 2, 2019·Nature Methods·Tonmoy ChakrabortyReto Fiolka
Jul 1, 2020·Nature Biotechnology·Min GuoHari Shroff
Sep 16, 2020·Nature Neuroscience·Aaron T KuanWei-Chung Allen Lee
Sep 28, 2020·Current Protocols in Neuroscience·David M YoungStephan J Sanders
Apr 29, 2020·Biomedical Optics Express·Michael A PinkertKevin W Eliceiri
Aug 11, 2019·Nature Methods·Vivien Marx
Nov 12, 2020·Lab on a Chip·Lisa F HorowitzAlbert Folch
Nov 10, 2020·Protein Science : a Publication of the Protein Society·Alexandra B SchroederKevin W Eliceiri
Oct 1, 2020·Bioinformatics·Romain Fernandez, Cédric Moisy
Nov 29, 2020·Nature Protocols·Hendrik A MessalAxel Behrens
Dec 9, 2020·Proceedings of the National Academy of Sciences of the United States of America·Alexander Franciscus van TolRichard Weinkamer
Dec 8, 2020·Biomedical Optics Express·Lindsey A BarnerJonathan T C Liu
Feb 17, 2021·Nature Biomedical Engineering·Jonathan T C LiuAnant Madabhushi
Mar 16, 2021·F1000Research·Christopher Schmied, Helena Klara Jambor
Mar 12, 2021·Bioinformatics·Friedrich PreusserStephan Preibisch
Mar 27, 2021·Molecular Systems Biology·Muge MolbayAli Ertürk
May 22, 2021·Nature Communications·Jennifer Oyler-YanivRoy Wollman
May 23, 2021·Nature Protocols·Kurt R WeissJan Huisken
Apr 17, 2021·Nature Biotechnology·Brian ClearyAviv Regev
Apr 30, 2020·Molecular Cell·Alexandra LewisThomas F Duchaine
May 18, 2021·Biomedical Optics Express·Nikita VladimirovStephan Preibisch
Jun 15, 2021·Progress in Biophysics and Molecular Biology·Gregory B SandsBruce H Smaill
Jul 6, 2021·Biomedical Optics Express·Cédric SchmidtJérôme Extermann
Jul 27, 2021·Advanced Science·Jungyoon OhnHyungil Jung
Jul 4, 2021·Progress in Biophysics and Molecular Biology·Adam L Tyson, Troy W Margrie
Jul 28, 2021·Nature Biotechnology·Fang XuGuo-Qiang Bi
Dec 17, 2020·ACS Chemical Neuroscience·Jiajia ZhaoHaitao Sun
Sep 9, 2021·Development·Nicola GrittiVikas Trivedi
Aug 20, 2021·Development·Mostafa Aakhte, Hans-Arno J Müller
Oct 2, 2021·Development·Alba Vieites-Prado, Nicolas Renier

❮ Previous
Next ❯

Methods Mentioned

BETA
light scattering
light microscopy

Software Mentioned

ImgLoader
Zeiss
Terastitcher
BigDataViewer
XUVTools
ImgLib2
BigStitcher
BioFormats
Fiji
AutoLoader

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Frontiers of Radiation Therapy and Oncology
I J Kalet
Nature Methods
Stephan PreibischPavel Tomancak
© 2021 Meta ULC. All rights reserved