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

[Mario Emmenlauer-3]

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 Confocal Microscopy List at
[hidden email] so interested readers may find
further responses in their list archive.

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Hi Mario,

I wrote a bead simulator some time ago, might this help? It can do any size you want for testing …

Cheers,
Stephan
---

Dr. Stephan Preibisch
Group Leader

Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
Building 89, 1.08b

email: [hidden email]<mailto:[hidden email]>
web: http://preibischlab.mdc-berlin.de

On 11. May 2017, at 12:36, Mario Emmenlauer <[hidden email]<mailto:[hidden email]>> wrote:

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 Confocal Microscopy List at
[hidden email]<mailto:[hidden email]> so interested readers may find
further responses in their list archive.

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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[Mario Emmenlauer-3]

Hi Stephan,

ah, I recall that you showed this at the hackaton! Completely
forgot about it! I will use this if I can not find real data, but
for the sake of the example I'd slightly prefer real data (i.e.
to see if there are differences to visualize tissue deeper inside
the sample, or maybe obscure data formats that impact the
data quality or rendering).

All the best,

    Mario



On 11.05.2017 12:58, [hidden email] wrote:

> Hi Mario,
>
> I wrote a bead simulator some time ago, might this help? It can do any size you want for testing …
>
> Cheers,
> Stephan
> ---
>
> Dr. Stephan Preibisch
> Group Leader
>
> Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine (MDC)
> Building 89, 1.08b
>
> email: [hidden email]<mailto:[hidden email]>
> web: http://preibischlab.mdc-berlin.de
>
> On 11. May 2017, at 12:36, Mario Emmenlauer <[hidden email]<mailto:[hidden email]>> wrote:
>
> 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

Viele Gruesse,

    Mario Emmenlauer


--
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Balanstr. 43                   mailto: memmenlauer * biodataanalysis.de
D-81669 München                          http://www.biodataanalysis.de/

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