Software for 3D and 4D analysis

[0000001ed7f52e4a-dmarc-request]

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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

[Mike Nelson]

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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
>

[Gary Laevsky]

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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:

> *****
> 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.
> *****
>
> 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
> >
>

--
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.

[Ann-W]

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*****

Hi Andreas

We went with Imaris as we got great support from them and have a load of licenses, plus it processes our spinning disk data well. The annual service fee isn't cheap and its still a fair bit of one image at a time. However we have the floating license and server version and our users can access it from 3 different buildings. A nuisance for our image analyst who has to go chasing around if someone presses the wrong button but very much appreciated by our users. Imaris also offers temporary licenses which is helpful for teaching and / or if you have a user who has a decent computer and needs to do a lot of processing in a short period of time. This way they get their results and the other facility users don't go crazy because this one person blocked up the analysis computer etc.

 We demo'd Arivis and really liked it - it did a great job with our light sheet data - but as others have said it is not a bargain option. I can't comment on the floating license options because we didn't get that far.

Hope that helps

Ann

Dr Ann Wheeler
Advanced Imaging Resource, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU
Working Pattern. Mon 9am - 2pm, Tues - Thurs 9am - 5pm.
E: [hidden email]
T: 0131 651 8665
W: http://www.igmm.ac.uk/imaging.htm


-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Andreas Bruckbauer
Sent: 13 November 2019 15:31
To: [hidden email]
Subject: Software for 3D and 4D analysis

*****
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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
The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

[Darran Clements]

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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:

> *****
> 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.
> *****
>
> 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
> >
>

--
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.

[Rosemary White]

*****
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*****

If you already use Fiji, it would be worth trialling freeware Ilastik - machine learning and segmentation for image analysis, plus meshlab - rendering of 3D data sets. I have only just started using them but they seem quite versatile. You do need enough RAM, etc. to handle large data sets within a reasonable timeframe.

cheers,
Rosemary

M: 61-0468966713
E: [hidden email]
________________________________________
From: Confocal Microscopy List [[hidden email]] on behalf of Mike Nelson [[hidden email]]
Sent: Thursday, 14 November 2019 3:04 AM
To: [hidden email]
Subject: Re: Software for 3D and4D analysis

*****
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.
*****

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
>

[Armstrong, Brian]

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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:[hidden email]] On Behalf Of Mike Nelson
Sent: Wednesday, November 13, 2019 8:05 AM
To: [hidden email]
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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Post images on https://urldefense.com/v3/__http://www.imgur.com__;!QQhUyc1sFJI!69GmjSXiuf6KDBT9SJu9hSmQ960esgy3RYhxIFV1FsHvz8QaYcIC8A-eqlKp4Kg$  and include the link in your posting.

*****



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:

> https://urldefense.com/v3/__http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy__;!QQhUyc1sFJI!69GmjSXiuf6KDBT9SJu9hSmQ960esgy3RYhxIFV1FsHvz8QaYcIC8A-emjFtKkw$ 

> 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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[Benjamin Smith]

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One other software package to consider is Avizo.  When we bought it, it was
one of the cheapest options, as well as one of the most powerful,
especially for large data.  Bonus points for the fact it lets you load and
display multiple datasets simultaneously, and even tune the shading to make
3D images especially clear for publications.  We also had Imaris, but we
found ourselves turning more often to Avizo, except for object tracking
,which Imaris is very good at.

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
>

--
Benjamin E. Smith, Ph. D.
Imaging Specialist, Vision Science
University of California, Berkeley
195 Life Sciences Addition
Berkeley, CA  94720-3200
Tel  [phone]
Fax [phone]
e-mail: [hidden email]
https://vision.berkeley.edu/faculty/core-grants-nei/core-grant-microscopic-imaging/

[Vincent Schoonderwoert]

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*Commercial response*

Dear CLS and Andreas,

Many users, many analysis questions and many preferences. With this in
mind, we like to add to this discussion another option. Many of you know
and may use Huygens for its deconvolution, but it is also possible to
add 3D-5D image analysis functions to the same user interface avoiding
file transfer and re-scaling of data. Analysis options are available for
a very affordable price and for many situations (beginners/expert users,
and floating or node-locked licenses). Best advise that we can give: ask
for free test versions of each package and see whether it fulfils your
needs and budget.

Best wishes,
Vincent




 
Join our webinar on 2D and 3D SMLM analysis
with Huygens LOCALIZER
Register here: https://svi.nl/WebinarInvitation
***********************************************
Vincent Schoonderwoert, PhD
Director Public Relations & Science
Scientific Volume Imaging
www.svi.nl
[phone]
***********************************************





On 13-11-19 23:33, Benjamin Smith 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.
> *****
>
> One other software package to consider is Avizo.  When we bought it, it was
> one of the cheapest options, as well as one of the most powerful,
> especially for large data.  Bonus points for the fact it lets you load and
> display multiple datasets simultaneously, and even tune the shading to make
> 3D images especially clear for publications.  We also had Imaris, but we
> found ourselves turning more often to Avizo, except for object tracking
> ,which Imaris is very good at.
>
> 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
>>
>

[Arvonn Tully]

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Post images on http://www.imgur.com and include the link in your posting.
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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:
> http://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy
> Post images on http://www.imgur.com and include the link in your posting.
> *****
>
> 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
> >
>

[Steffen Dietzel]

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*****

Am 13.11.2019 um 23:33 schrieb Benjamin Smith:
> One other software package to consider is Avizo.  When we bought it, it was
> one of the cheapest options, as well as one of the most powerful,
> especially for large data.  Bonus points for the fact it lets you load and
> display multiple datasets simultaneously,

I don't have much to add to what has been said, except maybe this: Yes,
one instance of Imaris will open only one data set. But you can open
several instances of Imaris in parallel. Whether this is a fun thing to
do or not will depend on the power of the hardware.

Best

Steffen

--

------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Biomedical Center (BMC)
Head of the Core Facility Bioimaging

Großhaderner Straße 9
D-82152 Planegg-Martinsried
Germany

http://www.bioimaging.bmc.med.uni-muenchen.de

[0000001ed7f52e4a-dmarc-request]

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

Many thanks for all the replies and good comments, I now got test licenses, a powerful computer and am happily testing. It turns out that professional software can be much faster (~20x) than Fiji for the same task, due to efficient multitasking? But actually measuring the speed is not so straightforward as small changes to the parameters can make a big difference in speed. Sometimes the whole analysis comes to a stop and one does not know where it is hanging... And pre-fabricated pipelines can be very inflexible.   best wishes  Andreas  -----Original Message-----
From: Steffen Dietzel <[hidden email]>
To: CONFOCALMICROSCOPY <[hidden email]>
Sent: Fri, 15 Nov 2019 9:37
Subject: Re: Software for 3D and 4D analysis

*****
To join, leave or search the confocal microscopy listserv, go to:
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Post images on http://www.imgur.com and include the link in your posting.
*****

Am 13.11.2019 um 23:33 schrieb Benjamin Smith:
> One other software package to consider is Avizo.  When we bought it, it was
> one of the cheapest options, as well as one of the most powerful,
> especially for large data.  Bonus points for the fact it lets you load and
> display multiple datasets simultaneously,

I don't have much to add to what has been said, except maybe this: Yes,
one instance of Imaris will open only one data set. But you can open
several instances of Imaris in parallel. Whether this is a fun thing to
do or not will depend on the power of the hardware.

Best

Steffen

--

------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Biomedical Center (BMC)
Head of the Core Facility Bioimaging

Großhaderner Straße 9
D-82152 Planegg-Martinsried
Germany

http://www.bioimaging.bmc.med.uni-muenchen.de

[Ariel, Pablo]

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Just wanted to comment that it is possible to open more than one image in a single Imaris instance.

This was introduced in Imaris 9.2 ("Add image" in the File menu; see video called "Loading Multiple Images and Alignment" in https://imaris.oxinst.com/versions/9-2 ). The applications mentioned in the video are to embed higher resolution or higher dimensional data in a--spatially-- larger dataset taken at lower resolution or with fewer dimensions, or to put things side by side. We've used it a bit for the latter: qualitative comparisons of a few different light-sheet datasets set side by side. I don't know how its performance compares with this functionality in other software, but it can be done.

Best,
Pablo


Pablo Ariel, Ph.D.
Assistant Professor
Director of the Microscopy Services Laboratory
Brinkhous-Bullitt Bldg B04
Department of Pathology and Laboratory Medicine
University of North Carolina at Chapel Hill
http://www.med.unc.edu/microscopy
Tel: [phone]



-----Original Message-----

I don't have much to add to what has been said, except maybe this: Yes, one instance of Imaris will open only one data set. But you can open several instances of Imaris in parallel. Whether this is a fun thing to do or not will depend on the power of the hardware.

Best

Steffen

--

------------------------------------------------------------
Steffen Dietzel, PD Dr. rer. nat
Ludwig-Maximilians-Universität München
Biomedical Center (BMC)
Head of the Core Facility Bioimaging

Großhaderner Straße 9
D-82152 Planegg-Martinsried
Germany

http://www.bioimaging.bmc.med.uni-muenchen.de