All posts by Felix Meyenhofer

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New Digital Silde-Scanner

We are glad to announce the addition of a NanoZoomer S60 to our core facility.

The NZ S60 is a slide scanner tailored towards research and superior as compared to the digital pathology workhorse, its predecessor the NanoZoomer HT+Fluo. The S60 supports multiple slide formats (single and double slides) and is well suited to acquire multi-channel fluorescent scans with a sensitive sCMOS camera.

The NZ S60 is recommended for fluorescence scans followed by object quantification and further processing while we suggest to use the NZ HT+Fluo for bright field scans or for simple fluorescent staining checks.

Finally, there was remarkable development concerning file formats. With the release of Bio-Formats 6.4, all the software using the Bio-Formats library – such as ImageJ, QPath, OMERO, etc. – have now the capacity to read a variety of NDPI files. Most notably NDPI files that use JPEG-XR compression are now supported. In contrast to the standard JPEG compression it is a lossless compression. We therefore recommend that NZ users change their profiles to use this standard.

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New image processing workstation

We are happy to announce that we have a new image processing workstation available in our core facility. Like the previous computer it is tailored for image processing:

  • 24 cores
  • 128 GB RAM
  • M2 SDD hard disks
  • big screen
  • CUDA capable graphics card
  • fast network (up to 800 MB/s)

The machine is optimised for large input-output operations with a lot of RAM, super fast hard drives and also a network connection that allows read and write 10 times (or more) faster on file servers than you could write on an external hard drive.

Currently the available software is ImageJ, Imaris and Amira. Other software will be installed upon request.

The machine is now bookable in IRIS.
Please use our image processing workstations via Remote Desktop Connection whenever possible and contact us, if you need assistance setting it up.

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Access of the core facility as of May 11th

According to the UNIFR-guidelines concerning COVID-19, the core facility will take steps towards normal operation again starting on May 11th.  Access will be possible for UNIFR researcher while following specific preventive measures, tailored for facility Users. The placards with necessary information will be posted on the entry doors of facility premises and next to the microscopes, respectively.

Beware that training sessions for the microscopes require additional preventive measures and therefore will be postponed until further notice. Please be patient until the facility staff found its new routine under the current circumstances.

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Booking System Migration

The core facility decided to switch booking systems. The new web application, OpenIRIS, is tailored for scientific core facilities and offers additional useful functionality (like coordination between multiple facilities) for users and also better fits the current technical requirements.

We imported all research groups and its members that were already using our facility during the first quarter of this year.
Users that already had training on a given instrument, but do not have the necessary privileges on IRIS to book a system, can use the training request functionality and leave a comment to get access in the new booking system too.

The new booking system takes over the following functionalities:

  • registration => handled via training requests
  • booking calendar
  • issue tracker

Go to new booking system page.

IP workstation RDC

You have to be sure the machine is running. Establish a VPN connection if connecting from outside UNIFR.

Windows

  1. Launch the application Remote Desktop connection
  2. Enter the PC name and connect.
  3. Enter your UNIFR credentials

Mac

  1. Launch the Microsoft Remote Desktop app. (You can get it from the app store)
  2. Menu > Connection >  Add Desktop
  3. Enter the PC name and click on the ‘Add’ button
  4. Double click on the computer that you just added
  5. You should be prompted for your UNIFR credentials

When you logout, just disconnect. Do not shutdown the system.

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HRM update – new look, new features

We updated our Huygens Remote Manager to the version 3.7.0. New features include obviously the new look, file formats can be mixed now and there are some improvements on how the deconvolution templates can be configured. The full list can be found on the huygens-rm.org.

There is also a webinar about the new HRM 3.7 made by Daniel from SVI.

Finally here is a reminder about our own installation of the HRM. You can find our site specific documentation on our bioimage website:
http://www3.unifr.ch/bioimage/it/software-list/huygens-2/

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ImarisViewer – 3D visualisation utility

Oxford Instruments released the ImarisViewer. It is a subset of the Imaris functionality, essentially constraint to the 3D visualisation capabilities. But it a free version, that allows you browse your datasets you processed with Imaris.

Windows users being part of SECMED or BIOL can install the ImarisViewer via the Baramundi Kiosk.

Mac users can find the installer on our download page (visible only from within the UNIFR domain)

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Amira/Avizo – new software license

Our facility together with  several departments of the SCIMED faculty was able to acquire  licenses for Thermo Fisher’s 3D visualisation and image analysis software.

While Avizo is destined more for applications in the field of material sciences, Amira is targeted towards life sciences. The software also allows for third party extensions. A curated collection of such extensions is hosted by provider itself.

This type of software is particularly useful for very large datasets (big, possibly time-resolved volumes). This type of task also has high requirements concerning computer hardware. Therefore we installed in on our best image processing workstation at this time. This computer is bookable like a normal instrument.

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Huygens Professional

Our image processing workstation is now equipped with Huygens Professional (desktop). Compared to our Huygens Remote Manager (HRM) the HuPro allows for more flexibility and provides some additional functionality.

The new HuPro desktop version of the Huygens software is intended to accelerate the optimization of the deconvolution parameter and do advanced image restoration using measured point spread functions (in contrast to the theoretical PSF).

This new license replaces the Huygens Essential that was previously accessible via remote desktop connection.