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Hi, I think it depends in part on what you want to accomplish. I personally prefer Imaris for 3D/4D quantification as it is easy to use and powerful and will measure just about anything you wish to measure. The cost is a drawback as Imaris is expensive in my opinion. Imaris support is great, but of course you have to pay for the great service. I still prefer Amira for some segmentation tasks and for movie making, and Amira has has great support. I was impressed with Arivis and my impression is that they could open any size data set and we opened data over a TB. Arivis seems well adapted to Zeiss czi files. My take on the VR is that it is "cool" but not too scientifically useful. I also thought that Arivis was surprisingly expensive. Amira also has VR capability and can export files in a format that a 3D printer can utilize (perhaps they all can by now?). I also like Image Pro Premier 3D just because I know IPP well and I am comfortable with the interface which is basically identical between the 2D and 3D platforms. Moreover, if cost is a consideration (and it always is) then IPP 3D may be a good choice for quantification in 3D.
*These are just my opinions and not facts. "Expensive" is always a relative term. The user (me in this case) may simply be more familiar with one software over another. For example Amira now has advanced quantification capabilities but I do not know them well because if I am doing that kind of work I simply open Imaris instead. Therefore, my opinion is biased.
**I completely agree with Mike Nelson below that stressed the importance of the hardware, and as he suggests, I purchased the video card that Imaris/Bitplane recommended for using their software. These companies have tech specialists that can help guide you in making these decisions.
Happy Imaging,
Brian Armstrong PhD
Associate Research Professor
Developmental and Stem Cell Biology
Diabetes and Metabolic Diseases
Director, Light Microscopy Core
Beckman Research Institute, City of Hope
-----Original Message-----
From: Confocal Microscopy List [mailto:[log in to unmask]] On Behalf Of Mike Nelson
Sent: Wednesday, November 13, 2019 8:05 AM
To: [log in to unmask]
Subject: Re: Software for 3D and 4D analysis
[Attention: This email came from an external source. Do not open attachments or click on links from unknown senders or unexpected emails.]
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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 <
[log in to unmask]> wrote:
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> Post images on https://urldefense.com/v3/__http://www.imgur.com__;!QQhUyc1sFJI!69GmjSXiuf6KDBT9SJu9hSmQ960esgy3RYhxIFV1FsHvz8QaYcIC8A-eqlKp4Kg$ 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
>
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