Posted by
Arvonn Tully on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Software-for-3D-and-4D-analysis-tp7590134p7590148.html
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Dear Mike,
I'm glad to hear that you like the 360 video export option.
On behalf of the team at Arivis, I'd like to correct an apparent
misunderstanding.
The visualization in Vision4d does **not** have an intrinsic limitation of
512^3.
By default Arivis Vision4d will render a the largest down sampled version
of the image which fits in graphics card memory. The downsampling is
dynamic to fit as much of the data set into current graphics card memory as
possible. This is intentionally done to maximize rendering speed on any
size graphics card. In principle you will experience interactive rendering
of large images even on a laptop with limited graphics memory.
Furthermore, Arivis Vision4d offers a dynamic level of detail rendering
mode which will display the raw data in the current viewing area, but due
to it's lower performance it is not enabled by default.
But there is no need to take my word for it, please take a look at some
recent papers which cite Arivis Vision4d as being used to render and
interactively
work with significantly larger images.
In particular please see:
Chakraborty, T., Driscoll, M.K., Jeffery, E. *et al.* Light-sheet
microscopy of cleared tissues with isotropic, subcellular resolution. *Nat
Methods* 16, 1109–1113 (2019) doi:10.1038/s41592-019-0615-4
and
Cai, R., Pan, C., Ghasemigharagoz, A. *et al.* Panoptic imaging of
transparent mice reveals whole-body neuronal projections and skull–meninges
connections. *Nat Neurosci* 22, 317–327 (2019) doi:10.1038/s41593-018-0301-3
Finally, I would like to echo what Gary L said -
Demo demo demo.
It is very important must strongly encourage everyone to do a thorough
test of analysis software, to ensure that it is meeting their specific
research requirements.
With that, please don't hesitate to email me at
[hidden email]
with any further Arivis Vision4d rendering questions or request for
demonstration and I would be happy to help!
Best Regards
Arvonn
----
On Wed, Nov 13, 2019 at 11:05 AM Mike Nelson <
[hidden email]> wrote:
> *****
> To join, leave or search the confocal microscopy listserv, go to:
>
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> *****
>
> We ended up going with Imaris, but I strongly recommend getting a free demo
> (they all should make one available) for your particular institute's area
> of interest or user model. There is usually a tradeoff between amount of
> options in terms of workflows and user interface accessibility/learning
> curve, so some of the choice may come down to whether the software is being
> dropped in the user's lap, or the core facility is running the analysis or
> guiding them through it. I have only demoed Arivis, and while the
> interactive 3D manipulation of volumes was neat, it was limited to a 512^3
> pixel volume at the time, which wasn't going to cut it as a useful tool.
> The one thing I *really *liked about Arivis that Imaris didn't have was the
> capacity to produce the 360 degree videos (search it on YouTube). It's the
> closest you can get right now to easily sharing a 3D volume, and can make
> for a great social media tool or intro to a lab's website. Imaris also
> doesn't seem to have much in the way of machine learning or deep learning
> algorithms currently built in (paint objects, find all objects that look
> like the painted objects), though you could build your own with MATLAB.
>
> In the end, we went with Imaris due to the workflow and ease of use for the
> core facility customers. It could be used for fairly complex analyses
> with *relatively
> *little training and has a reasonably clean user interface. Most commercial
> software can now handle very large images these days, but there is a
> difference between "handles" and "can populate with objects or do image
> analysis on," which was something we ran into with Amira. It could load the
> images, but you couldn't actually analyze the full volume (at the time).
>
> I haven't tried Aivia.
>
> The computer you want to run these programs on can also have a significant
> impact on whether they are actually useful to you, so plan on either having
> or also purchasing a nice computer (and with a compatible video card, check
> with the vendor as far as which cards work best).
>
> Most of these tools are under development, so who knows what will be the
> best next year!
>
> On Wed, Nov 13, 2019 at 7:32 AM Andreas Bruckbauer <
>
[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 am interested to hear your opinions regarding image
> analysis
> > software for processing of larger datasets 3D and 4D datasets. How
> > do Imaris, Arivis and Aivia (maybe others?) compare? I am aware of Icy
> and
> > Fiji, but often find that we are hitting the limits when working with
> large
> > files e.g. 20 GB - 50 GB, but not the TB range yet. On the other hand we
> > often have to go back to Fiji to do some more complex analysis. This
> would
> > be for a light microscopy facility setting. Best wishes Andreas
> >
>