high-res 3D multi-channel datasets for download?

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Mario Emmenlauer Mario Emmenlauer
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high-res 3D multi-channel datasets for download?

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Dear All,

I'd like to evaluate the available open source 3D volume rendering
software packages. But to challenge the software, I would like to come
close to the limits of current dataset size in X/Y/Z/C, i.e. have
high 3D resolution with multiple channels. Are there datasets with
very high resolution available? Interesting is either a big volume
like 1024 x 1024 x 1024 or more, or a large X/Y area with some Z-depth
like 10000 x 10000 x 10 or more. If there are multiple channels its
even better! I do not mind so much the sample type and data source,
confocal or super-resolution or anything is interesting.

Currently with the help of the list archive, I found the excellent
resource https://loci.wisc.edu/software/sample-data and this gives a
good start, but the maximum Z resolution there is 70 planes on a 512^2
image dataset (albeit with time).

All the best,

    Mario Emmenlauer


PS: I will cross-post this to the ImageJ interest group at
[hidden email] so interested readers may find further responses
in their list archive.
Romain Laine Romain Laine
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Re: high-res 3D multi-channel datasets for download?

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Hi Mario,
If you are interested in visualization of 3D data, I suggest you have a
look at this Nature photonics correspondence
http://www.nature.com/nphoton/journal/v11/n2/full/nphoton.2016.273.html?WT.feed_name=subjects_physics

It's not really for big data visualization but is very powerful for sharing
and distributing data online.

Also, if you want some large 3D data with specific resolution, pixel number
etc., the easiest might be to generate them in silico (using MATLAB or
similar), depending on how much experience you have in coding, it can be
relatively easy.

Cheers,

Romain

--
Dr. Romain Laine, PhD in Biophotonics
Laser Analytics Group
Department of Chemical Engineering and Biotechnology
University of Cambridge
West Cambridge Site
Philippa Fawcett Drive
Cambridge
CB3 0AS


On Thu, May 11, 2017 at 11:35 AM, Mario Emmenlauer <[hidden email]>
wrote:

> *****
> To join, leave or search the confocal microscopy listserv, go to:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> Dear All,
>
> I'd like to evaluate the available open source 3D volume rendering
> software packages. But to challenge the software, I would like to come
> close to the limits of current dataset size in X/Y/Z/C, i.e. have
> high 3D resolution with multiple channels. Are there datasets with
> very high resolution available? Interesting is either a big volume
> like 1024 x 1024 x 1024 or more, or a large X/Y area with some Z-depth
> like 10000 x 10000 x 10 or more. If there are multiple channels its
> even better! I do not mind so much the sample type and data source,
> confocal or super-resolution or anything is interesting.
>
> Currently with the help of the list archive, I found the excellent
> resource https://loci.wisc.edu/software/sample-data and this gives a
> good start, but the maximum Z resolution there is 70 planes on a 512^2
> image dataset (albeit with time).
>
> All the best,
>
>     Mario Emmenlauer
>
>
> PS: I will cross-post this to the ImageJ interest group at
> [hidden email] so interested readers may find further responses
> in their list archive.
>
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