NetNotes


on the microscope computer. Our users must transfer all their data to the server and empty the local drive before they turn off the system. Any data found on the local drive is immediately deleted. On top of that, we have a Virtual Desktop Infrastructure (VDI) consisting of 2 powerful Remote Desktop Servers (256GB RAM, 2 Graphic cards with 16 GB RAM each) that are maintained by the university and are located in the server room. Tese are also expandable/upgradable. We are not in charge of them but we do enjoy using them! Tese machines and the server are accessible remotely via soſtware called VMWare. Tis allows us to log in to the VDI from any computer (even a mobile phone). Logging to the VDI creates a virtual Windows desktop on which we have Fiji, Cell Profiler, Imaris, NIS elements, and MATLAB. Several users can log in to each RDS at the same time. Having an infra- structure that is centrally maintained has simply changed our (my) microscopy life! Sylvie Le Guyader sylvie.le.guyader@ki.se


My current institution mostly uses cloud solutions, due to


University-wide agreements with cloud providers. As pointed out this isn’t great for lab-wide aggregating and archiving. My previous insti- tution also had a centralized PB-scale Isilon server for rapid-access needs, plus an offline tape backup service for long term archiving. Tis has a great economy of scale - and it made it very easy for us to implement OMERO, which is a fantastic image data management package! However not many institutions can support that kind of centralized data handling. Timothy Feinstein tnf8@pitt.edu


My experience is that many cloud infrastructures do not allow


the upload of files that are larger than 4 GB. Not sure if it is true for all of them. On top of that, there is of course the problem of speed to upload and need to download again to analyze the data. With a local infrastructure, you skip this time which is considerable if one has a light sheet system. Sylvie Le Guyader sylvie.le.guyader@ki.se


We are looking into setting up a virtual machine to run Imaris.


You mention you are doing this now and so I am wondering how the licensing works for this? Do you have a campus-wide license or just a single license for Imaris? Tank you! I have reached out to them but have not heard back about whether or not it is possible to do this. Holly L. Aaron hollya@berkeley.edu


Yes we have been running Imaris on a virtual desktop infra- structure. We love it! Tis is a clear improvement


for everyone.


You need a floating license manager. Another facility at KI had one but had no VDI so we are merging our licenses. We have 14 Imaris licenses. In the long run it would be really great if we could merge all or most of them. Bitplane is quite pleased with the process as far as I know and they are very helpful. Te first challenge was to with all the license own- ers. Many of these licenses had not been updated for ages. Grouping all licenses gives great (up to 70 or 80%) discount on upgrades and service contracts so on top of the great advantage of having a super infrastructure accessible to users from anywhere and maintained by the university IT people, there is money to be saved. Also in our case all modules are pulled together instead of being associated with one license so this adds flexibility. But I know that there are many ways to run university-wide licenses. Each license could be instead associated with one group of users. We see a great advantage in pulling every- thing. For Bitplane there is a clear advantage when old licenses are upgraded and are being used again. Te second challenge is to find a way to balance the cost models:


At our facility, those who have paid the (usually yearly) membership have access to Imaris for free. Te other facility makes people pay per hour. I think that once you have migrated to a virtual infrastructure


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of high quality, there is no turning back. :) Sylvie Le Guyader sylvie. le.guyader@ki.se


Microscope Slide Scanners Confocal Microscopy Listserver We are looking for a slide scanner and have a very short deadline.


We need to screen whole brain slices with 3–4 fluorescent labels, z stack capabilities, and a fast overview image of a whole brain slice. We would like to image 6 slides and obtain an overview image of each slide to assess them for further confocal study. We are currently looking at the Olympus SLIDEVIEW™ VS200 or better version. Agnes Janoshazi 00000455be8c116a-dmarcrequest@lists.umn.edu


My own observation with several models of slide scanner is


that sample preparation and handling is probably more important than the equipment itself. Most scanners use some flavor of autofo- cus, and the method used may or may not be compatible with the various quirks of your specific samples. If you are using a multi-slide handling system, the type of slides you use, or any treatment during your process, may literally gum up the feed mechanism that trans- fers slides from storage to the imaging area. So in short, you really won’t know how a system is going to perform until you try your spe- cific samples on it. If you do get any advice from forum members, I’d also ask exactly how they prepare their samples and how the system handles things like misaligned coverslips and errant smudges. Craig Brideau craig.brideau@gmail.com


You will have to rank-order the most important features for


your needs (z-stacking, automated scanning of 10s of slides or 100s of slides, 4 fluorescent channels, multi-user friendly, fast overview of whole slides, etc.) because no system does everything. I have used a number of top-of-the-line fluorescent slide scanners. Here are some options you may want to follow up on with providers: Vectra Polaris (our current workhorse in the lab): User-friendly,


very fast, no z-stack, not very flexible (pretty locked-down in order to make it user-friendly). Zeiss AxioScan Z1 slide scanner: Like the Polaris it also takes


slides in holders, and like the Polaris can scan many sides at a time. Zeiss has soſtware to co-register across platforms, which may be very helpful for your specific need of matching a position from a slide scan to a more detailed confocal stack. Olympus SlideView VS200: Tis went on sale very recently (press


release Oct 31st 2019 - https://www.olympus-global.com/news/2019/ nr01430.html) so I don’t think many have had a chance to use it, but it is similar in format to the Zeiss AxioScan Z1. Keyence BZX-810: I’m including this because it has a holder for


imaging 3 microscope slides at a time, and you can take 4-color fluo- rescent z-stacks across entire slides quickly if at low magnification (like 4×). It is also very flexible to do a number of other things, and accepts a variety of microscope objectives. It is relatively user friendly, and you only mentioned needing to image half a dozen slides. Te systems above are for scanning in slides at much larger volumes and are maybe not what you need in the end unless you’re digitizing every section through whole rodent brains. You could also buy 3 of these for the price of any of the others on the list. BUT, it is not strictly a slide scanner, and will not perform the task of scanning slides nearly as fast or as easily as the others on this list. Andrew Woolley ajwoolley@ gmail.com


I don’t know about the VS200, but we have 3 original Olympus


dotSlides (brightfield) and an Olympus VS110 with fluorescence as well as a bright-field 3D Histech panorama scan. Te VS110 is about


www.microscopy-today.com • 2020 March


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