NetNotes


Edited by Bob Price University of South Carolina School of Medicine Bob.Price@uscmed.sc.edu


Selected postings are from discussion threads included in the


Microscopy (http://www.microscopy.com) and Confocal Microscopy (https://lists.umn.edu/cgi-bin/wa?A0=confocalmicroscopy) listserv- ers from September 1, 2019 to December 31, 2019. Postings may have been edited to conserve space or for clarity. Complete listings and subscription information can be found at the above websites.


Software for 3D and 4D Analysis Confocal Microscopy Listserver I am interested in reading your opinions regarding image anal-


ysis soſtware for processing of large 3D and 4D datasets. How do Imaris, Arivis, and Aivia (maybe others?) compare? I am aware of Icy and Fiji, but oſten 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 oſten have to go back to Fiji to do some more complex analysis. Tis is for a light microscopy facility setting. Best wishes. Andreas Bruckbauer a.bruckbauer@imperial.ac.uk


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. Tere is usually a tradeoff between the amount of options in terms of workflow and user interface accessibility/learning curve, so some of the choice may come down to whether the soſtware 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 manipu- lation 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. Te one thing I *really* like about Arivis that Imaris does not have is the capacity to produce 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 com- plex analyses with *relatively* little training and has a reasonably clean user interface. Most commercial soſtware 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). Te 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 having g a nice computer with a compatible video card. Most of these tools are under development, so who knows what will be the best next year! Mike Nelson msnelson@gmail.com


We ended up going with Arivis. It’s the only soſtware that didn’t


crash on our multi TB datasets. I also must say, the support from Ari- vis has been really good as well. It’s expensive though … As I’m sure you know (and has been said), demo, demo, demo … Gary Laevsky glaevsky.lists@gmail.com


If you already use Fiji, it would be worth trialling freeware


Ilastik—machine learning and segmentation for image analysis, plus meshlab and 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. Rosemary White rosemary.white@anu.edu.au


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. Te annual service fee isn’t cheap and it is 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. Tis 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 did demo 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. Ann Wheeler Ann.Wheeler@ igmm.ed.ac.uk


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, powerful, and will measure just about anything you wish to measure. Te 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 making mov- ies, and Amira has great support. I was impressed with Arivis and my impression is that they could open any size data set as 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 basi- cally 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. *Tese are just my opinions and not facts. “Expensive” is always a relative term. Te user (me in this case) may simply be more familiar


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doi:10.1017/S1551929519001366


www.microscopy-today.com • 2020 March


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