Combining serial sections in one volume
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Combining serial sections in one volume
 
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Dear list
this is quite a basic question: I have some serial sections of an organelle that I took in a TEM. I want to combine them in a volume, but so far I was not successful. Could anyone give me an advice on how to do that? Thanks! Cheers Leo -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Combining serial sections in one volume
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Hi Leo,
You can try IMOD software from Boulder Laboratory http://bio3d.colorado.edu/imod/? It is designed to do 3D reconstruction from electronic tomography or serial sections. Philippe Le 11/12/2013 19:54, Leandro Lemgruber a écrit : > Dear list > > this is quite a basic question: > I have some serial sections of an organelle that I took in a TEM. I > want to combine them in a volume, but so far I was not successful. > Could anyone give me an advice on how to do that? > > Thanks! > > Cheers > > Leo > > -- > ImageJ mailing list:http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Combining serial sections in one volume
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Dear Philippe
I have tried, but the result was not good at all. Not like when I have tomograms. Cheers On Thu, Dec 12, 2013 at 4:33 AM, Philippe Mailly <[hidden email]> wrote: > Hi Leo, > > You can try IMOD software from Boulder Laboratory > http://bio3d.colorado.edu/imod/? It is designed to do 3D reconstruction from > electronic tomography or serial sections. > > > Philippe > > Le 11/12/2013 19:54, Leandro Lemgruber a écrit : >> >> Dear list >> >> this is quite a basic question: >> I have some serial sections of an organelle that I took in a TEM. I >> want to combine them in a volume, but so far I was not successful. >> Could anyone give me an advice on how to do that? >> >> Thanks! >> >> Cheers >> >> Leo >> >> -- >> ImageJ mailing list:http://imagej.nih.gov/ij/list.html >> > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- Research Support Specialist Electron Microscopy Resource Center The Rockefeller University 1230 York Avenue New York, NY 10065 USA -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Combining serial sections in one volume
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Dear Leo,
Have a look at those papers Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomancák, Pavel As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets Bioinformatics, 26, no. 12, pp. 57-63, (2010) Saalfeld, Stephan; Fetter, Richard; Cardona, Albert; Tomancak, Pavel Elastic volume reconstruction from series of ultra-thin microscopy sections. Nat. Methods, 9, no. 7, pp. 717-720, (2012) Cardona, Albert; Saalfeld, Stephan; Schindelin, Johannes; Arganda-Carreras, Ignacio; Preibisch, Stephan W.; Longair, Mark; Tomancak, Pavel; Hartenstein, Volker; Douglas, Rodney J TrakEM2 Software for Neural Circuit Reconstruction. PLoS ONE, 7, no. 6, (2012) All software is available in Fiji. All the best PAvel ----------------------------------------------------------------------------------- Pavel Tomancak, Ph.D. Group Leader Max Planck Institute of Molecular Cell Biology and Genetics Pfotenhauerstr. 108 D-01307 Dresden Tel.: +49 351 210 2670 Germany Fax: +49 351 210 2020 email: [hidden email] homepage: http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html twitter: @PavelTomancak ----------------------------------------------------------------------------------- On Dec 12, 2013, at 10:02 PM, Leandro Lemgruber <[hidden email]> wrote: > Dear Philippe > > I have tried, but the result was not good at all. Not like when I have > tomograms. > > Cheers > > > On Thu, Dec 12, 2013 at 4:33 AM, Philippe Mailly > <[hidden email]> wrote: >> Hi Leo, >> >> You can try IMOD software from Boulder Laboratory >> http://bio3d.colorado.edu/imod/? It is designed to do 3D reconstruction from >> electronic tomography or serial sections. >> >> >> Philippe >> >> Le 11/12/2013 19:54, Leandro Lemgruber a écrit : >>> >>> Dear list >>> >>> this is quite a basic question: >>> I have some serial sections of an organelle that I took in a TEM. I >>> want to combine them in a volume, but so far I was not successful. >>> Could anyone give me an advice on how to do that? >>> >>> Thanks! >>> >>> Cheers >>> >>> Leo >>> >>> -- >>> ImageJ mailing list:http://imagej.nih.gov/ij/list.html >>> >> >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > > -- > Research Support Specialist > Electron Microscopy Resource Center > The Rockefeller University > 1230 York Avenue > New York, NY 10065 USA > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Combining serial sections in one volume
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Dear Pavel
Sorry for the late reply. Thank you for the references and about the software. It works :) Cheers -- Leandro Lemgruber > On Dec 12, 2013, at 4:15 PM, Pavel Tomancak <[hidden email]> wrote: > > Dear Leo, > > Have a look at those papers > > Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomancák, Pavel > As-rigid-as-possible mosaicking and serial section registration of large ssTEM datasets > Bioinformatics, 26, no. 12, pp. 57-63, (2010) > > Saalfeld, Stephan; Fetter, Richard; Cardona, Albert; Tomancak, Pavel > Elastic volume reconstruction from series of ultra-thin microscopy sections. > Nat. Methods, 9, no. 7, pp. 717-720, (2012) > > Cardona, Albert; Saalfeld, Stephan; Schindelin, Johannes; Arganda-Carreras, Ignacio; Preibisch, Stephan W.; Longair, Mark; Tomancak, Pavel; Hartenstein, Volker; Douglas, Rodney J > TrakEM2 Software for Neural Circuit Reconstruction. > PLoS ONE, 7, no. 6, (2012) > > All software is available in Fiji. > > All the best > > PAvel > > ----------------------------------------------------------------------------------- > Pavel Tomancak, Ph.D. > > Group Leader > Max Planck Institute of Molecular Cell Biology and Genetics > Pfotenhauerstr. 108 > D-01307 Dresden Tel.: +49 351 210 2670 > Germany Fax: +49 351 210 2020 > email: [hidden email] > homepage: http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html > twitter: @PavelTomancak > ----------------------------------------------------------------------------------- > > > > > >> On Dec 12, 2013, at 10:02 PM, Leandro Lemgruber <[hidden email]> wrote: >> >> Dear Philippe >> >> I have tried, but the result was not good at all. Not like when I have >> tomograms. >> >> Cheers >> >> >> On Thu, Dec 12, 2013 at 4:33 AM, Philippe Mailly >> <[hidden email]> wrote: >>> Hi Leo, >>> >>> You can try IMOD software from Boulder Laboratory >>> http://bio3d.colorado.edu/imod/? It is designed to do 3D reconstruction from >>> electronic tomography or serial sections. >>> >>> >>> Philippe >>> >>> Le 11/12/2013 19:54, Leandro Lemgruber a écrit : >>>> >>>> Dear list >>>> >>>> this is quite a basic question: >>>> I have some serial sections of an organelle that I took in a TEM. I >>>> want to combine them in a volume, but so far I was not successful. >>>> Could anyone give me an advice on how to do that? >>>> >>>> Thanks! >>>> >>>> Cheers >>>> >>>> Leo >>>> >>>> -- >>>> ImageJ mailing list:http://imagej.nih.gov/ij/list.html >>> >>> >>> -- >>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html >> >> >> >> -- >> Research Support Specialist >> Electron Microscopy Resource Center >> The Rockefeller University >> 1230 York Avenue >> New York, NY 10065 USA >> >> -- >> ImageJ mailing list: http://imagej.nih.gov/ij/list.html > > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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