Re: Software for 3D and 4D analysis

Posted by Darran Clements on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Software-for-3D-and-4D-analysis-tp7590134p7590137.html

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We are currently looking at DRVision Aivia, seems interesting, machine learning and deep learning, segmentation etc. Been watching its development for some time so trying to do some processing in earnest with it at the moment. The workshop we had today went down well, so will be interesting to see what it can do with some real use cases.

Darran Clements

Imaging Facility Assistant
Wellcome-MRC  Stem Cell Institute
Jeffrey Cheah Biomedical Centre
Cambridge Biomedical Campus
University of Cambridge
Puddicombe Way
Cambridge
CB2 0AW

[hidden email]
01223 760 201

-----Original Message-----
From: Confocal Microscopy List <[hidden email]> On Behalf Of Gary Laevsky
Sent: 13 November 2019 16:26
To: [hidden email]
Subject: Re: Software for 3D and 4D analysis

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We ended up going with Arivis.  It's the only software that didn't crash on our multi TB datasets.

I also must say, the support from Arivis has been really good as well.

It's expensive though ...

As I'm sure you know (and has been said), demo demo demo ...

On Wed, Nov 13, 2019 at 11:05 AM Mike Nelson <[hidden email]> wrote:

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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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> > 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
> >
>

--
Best,

Gary Laevsky, Ph.D.
Director, Confocal Imaging Facility
Nikon Center of Excellence
Co-Founder, North Atlantic Microscopy Society (NAMS) https://namsmicroscopy.com/ Dept. of Molecular Biology Washington Rd.
Princeton University
Princeton, New Jersey, 08544-1014
(O) 609 258 5432
(C) 508 507 1310

North Atlantic Microscopy Society Annual Meeting at Princeton University, Nov. 1, 2019.