Posted by
Mike Nelson on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Software-for-3D-and-4D-analysis-tp7590134p7590135.html
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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:
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>
> 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
>