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Amira/Avizo can handle large datasets rather nicely, but they need a computer system scaled to the scope of the data set. For example, to get Amira/Avizo to run at full speed with files that are several GBs in size, we use a dual motherboard server with an 8 core processor each and currently 64GB of RAM (although this can be expanded to over 300GB if necessary).
As we have both Avizo and Imaris, I can tell you that Avizo eats up more RAM than Imaris per dataset, but that for what we do, Avizo multi-threads more tasks than Imaris. Avizo also gives extensively more control over movie creation and shaded rendering allowing for top-quality images and movies, while Imaris has an intuitive user interface when it comes to quantitative image analysis and movie production.
All in all, I would recommend simply demoing both pieces of software, and see which more reflects your needs. If you need to publish a lot of complex three-dimensional data, than Avizo will give you many more options on achieving an optimal 3D effect, while if you need a lot of statistical quantitation and don't want to spend a lot of time training users, then Imaris is better. In short, these two software packages play on their own strengths and are in no way redundant, which is why in our facility we have both. We use Avizo primarily for generating final images and cover photos, as well as highly complex/abstract image analysis. We use Imaris for nearly everything in between. We've even done some image processing projects that are started in FIJI, then further processed in Avizo, before doing final quantitation in Imaris, playing on each programs' strengths.
One other key note, Avizo can overlay images of different dimensions, and in different positions relative to one another. It can also allow for multiple separate datasets to be shown simultaneously. Imaris can sort of do this by opening multiple instances of the software, but it still makes direct comparison across images a bit harder, and our computer can only open 4 instances before the system crashes. So, if you would like to compare many different images simultaneously, Avizo can do this better, although FIJI can out perform both if you know how to structure your question correctly.
Hope this helps,
Ben Smith
Benjamin E. Smith, Ph.D.
Samuel Roberts Noble Microscopy Laboratory
Research Scientist, Confocal Facility Manager
University of Oklahoma
Norman, OK 73019
E-mail: [log in to unmask]
Voice 405-325-4391
FAX 405-325-7619
http://www.microscopy.ou.edu/
________________________________________
From: Confocal Microscopy List [[log in to unmask]] on behalf of Mark Scott [[log in to unmask]]
Sent: Thursday, August 20, 2015 6:31 PM
To: [log in to unmask]
Subject: Re: Arivis vs Imaris
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Does anyone have any experience with AMIRA with regards to handling large data-sets? I've had some experience in the past but that was many years ago and much smaller file sizes than we are handling these days. We are assessing options at the moment so would be keen to hear thoughts on AMIRA as it compares to the other two.
Thanks
Mark Scott
Specialist for Intra-vital and Live Cell Imaging
Centre for Dynamic Imaging
The Walter & Eliza Hall Institute
1G Royal Parade, Parkville
Victoria 3052, Australia
----- Original Message -----
From: "Davide Accardi" <[log in to unmask]>
To: [log in to unmask]
Sent: Thursday, 20 August, 2015 5:37:28 PM
Subject: Re: Arivis vs Imaris
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Hi Simon,
We extensively use light-sheet technology, thus we are big producer of large 4D datasets.
Because of the difficulties in handling big data, we have tested several softwares included Arivis.
As Douglas already said, Arivis is unbeatable in handling big data, even when working with small laptops.
This software is most likely the best tool to visualize and render your movies. However, its analysis capacity is limited to 2D data.
Indeed a 3D tracking tool is completely absent and this results in the fact that one can visualize 3D data but cannot extract information from them.
Surely the software gives the possibility to create custom made analysis tools by scripting in python, but this becomes very complicated for us, not feasible for a multi-user environment, and in my opinion decreases the ratio quality/price.
Regarding Imaris, my experience goes in the opposite direction.
In fact with this software one is limited in the amount of data that can be visualized and working with light-sheet files becomes challenging. On the other hand, you have advanced tools to follow particle in 3D and quantitatively extract the informations that you need.
I hope this helps.
Best,
Davide
--
Dr. Davide Accardi
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany
Phone: +49 351 210-2084
On Aug 19, 2015, at 10:37 PM, Douglas Richardson 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.
> *****
>
> Hi Simon,
>
> We've been working with arivis for awhile now and have been impressed with
> the software's ability to handle big data (TBs). We no longer have to
> worry about down sampling data, cropping fields of view, removing time
> points, etc.to enable our processing post-imaging. The only limitation for
> our experiments now is storage space.
>
> I feel arivis excels as rendering and visualization; however, as it is
> still a new product, they do not have as extensive a processing library as
> some other programs. Fortunately, the company has been very responsive to
> address our needs in this area and I'm hoping this will keep up as their
> customer base grows.
>
> -Doug
>
> Disclosure - I have no financial interests in arivis, but I have
> co-authored some abstracts/awards with them.
>
>
>
>
>
>
>
> On Wed, Aug 19, 2015 at 12:01 PM, simon watkins <[log in to unmask]> 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.
>> *****
>>
>> Folks, we are heavy users of Imaris. I came across Arivis4D
>> (http://vision.arivis.com/en/arivis-Vision4D) while looking at the wish
>> list for a faculty
>> recruit. Can anyone make a useful comparison for me for use in our
>> optical sectioning
>> world. Seems like an interesting solution from the website.
>> S
>>
>> Simon Watkins Ph.D
>> Distinguished Professor and Vice Chair Cell Biology
>> Professor Immunology
>> Director Center for Biologic Imaging
>> University of Pittsburgh
>> Bsts 225 3550 terrace st
>> Pittsburgh PA 15261
>> [log in to unmask]
>> Www.cbi.pitt.edu
>> 412-352-2277
>>
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