Arivis vs Imaris
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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 [hidden email] Www.cbi.pitt.edu 412-352-2277 |
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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 <[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. > ***** > > 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 > [hidden email] > Www.cbi.pitt.edu > 412-352-2277 > |
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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, Same experience as Doug. Arivis really pushes to get some market share from Imaris/Volocity/Amira. We had the arivis-guys at our institute for a 3-day-workshop just a few weeks ago and we did an intense assessment of the software. Besides the pro w.r.t. big data, some additional interesting points (subjective of course): #1 It has an advanced 'Undo'-function - via a processing history timeline you can instantaneously jump back to any point during the workflow (very handy for iterative image processing development) #2 Advanced import function - we had a single czi-file with multiple positions, many time points plus so called experimental blocks (see ZEN's experiment designer module), not even ZEN could open it and the Zeiss Service is still struggling with it - with the advanced import function in arivis we were able to reverse-engineer the file structure and by that arivis could open it #3 Timelapse analysis - the included time-lapse analysis module looked very advanced (manual, semi-automatic, and automatic tree reconstruction) - plots size/shape/fluorescence over time etc. The processing library is indeed still limited (OTSU and friends are on-board of course). But I think it can keep up with Imaris in the meantime. An interesting fact: they plan to implement a generic interface for external software (e.g. Python, Matlab, ImageJ), which allows to use own processing filters along the workflow. Another positive feature seems the general fast response time of arivis. I actually heard that in some cases they even put together an entire workflow if a certain user simply does not know how to analyse his images. In a nutshell: definitely worth testing, perhaps worth buying. best, Steffen On Wednesday, August 19, 2015 22:37 CEST, Douglas Richardson <[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. > ***** > > 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 <[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. > > ***** > > > > 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 > > [hidden email] > > Www.cbi.pitt.edu > > 412-352-2277 > > |
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In reply to this post by Douglas Richardson
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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 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 <[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. >> ***** >> >> 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 >> [hidden email] >> Www.cbi.pitt.edu >> 412-352-2277 >> |
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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. ***** 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" <[hidden email]> To: [hidden email] Sent: Thursday, 20 August, 2015 5:37:28 PM Subject: Re: Arivis vs Imaris ***** 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 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 <[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. >> ***** >> >> 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 >> [hidden email] >> Www.cbi.pitt.edu >> 412-352-2277 >> ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ |
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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. ***** 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: [hidden email] Voice 405-325-4391 FAX 405-325-7619 http://www.microscopy.ou.edu/ ________________________________________ From: Confocal Microscopy List [[hidden email]] on behalf of Mark Scott [[hidden email]] Sent: Thursday, August 20, 2015 6:31 PM To: [hidden email] Subject: Re: Arivis vs Imaris ***** 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. ***** 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" <[hidden email]> To: [hidden email] Sent: Thursday, 20 August, 2015 5:37:28 PM Subject: Re: Arivis vs Imaris ***** 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 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 <[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. >> ***** >> >> 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 >> [hidden email] >> Www.cbi.pitt.edu >> 412-352-2277 >> ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. ______________________________________________________________________ |
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In reply to this post by Watkins, Simon C
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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, For my work I mainly use light-sheet microscopy and therefore have to analyse large 4D data sets. Arivis, as mentioned in previous posts, is very good in handling big data. However, Arivis does not just offer nice visualisation but also good tools for analysis that come with a user-friendly interface. Our work focuses on the systematic and quantitative analysis of chromosome behaviour over time and in fact we specifically bought Arivis for 4D tracking of our big data sets. The software has very nice tools for image filtering, 3D segmentation and 3D tracking of particles. In addition Arivis offers a very good track editor which allows manual correction of potential segmentation and tracking errors if required. Those manual corrections are currently carried out in the 2D viewer but the next release of Arivis (coming out in the second half of this year) will support manual annotation of objects and creation of tracks in the 3D viewer as well. In addition to the comprehensive list of analysis tools Arivis also offers a python editor to allow the implementation of custom made scripts which gives a lot of flexibility. Let me know if you should have any further questions. Best wishes, Judith --------------------------------------------------------------------------- Judith Reichmann, PhD Ellenberg Group Cell Biology and Biophysics Unit European Molecular Biology Laboratory (EMBL) Meyerhofstraße 1 69117 Heidelberg (Germany) Tel: +49 6221 387-8802 email: [hidden email] |
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In reply to this post by Douglas Richardson
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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. ***** Hello, I have some limited experience of Arivis, which I used briefly for exploring out 200 GB to 1 TB data sets. My feeling was that it was useful for making attractive visualisations (e.g. to make a movie for a talk) but it added little for actually analyzing data (i.e. extracting information on which we can do statistics). This may have changed by this point, as I tried it a few months ago. Of course YMMV, but I find analyses of these large data comes in two flavours: 1) Extracting information from each high-resolution x/y plane. This doesn't require "3-D" visualisation. It just requires the section to be loaded into RAM and features extracted. We just ensure we have about 2 to 5 GB of RAM per core and do everything in MATLAB, Python, or even Icy. 2. The second set of analyses I find myself doing involves quantification of large-scale anatomical features in the whole volume. This might involve stuff like registering volumes to each other or tracing large features. If the original resolution was, say, 0.5 microns per pixel, these large-scale analyses work at the level of, say, 25 microns per pixel. For these analyses I prefer to simply down-sample the whole volume and load it into RAM and use the most applicable analysis approach. -- Rob Campbell Mrsic-Flogel Group Basel Biozentrum |
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