Category Archives: Equipment

Information concerning the microscopes and image processing computers.

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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.

ip-ws-gottéron

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.

hrm-3.7-results-screenshot

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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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.

avizio_argolight-screenshot

HuPro44_2

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.

threadripper

New Image Analysis Workstation

For those who spent a lot of time waiting for the computer to finish some image analysis task, we acquired a new desktop computer that might help remedy this loss of time. This new computer has a hardware configuration for large datasets that require computationally intensive processing.
You can find more details on number cruncher’s page. This workstation is henceforth available for all facility users.

omero_fpbioimage_screenshot

OMERO update

We updated our OMERO.server from 3.3.1 to 3.3.5

During the upgrade we optimized the server’s software dependencies for optimal performance.

In case your desktop clients do not connection to the server anymore, please update the OMERO.insight on you computer too. You find instruction and the download of the pre-configured clients on our web-site.

omero 5.3.5 upgrade

There is also a new goodie: FPBioimage is a 3D viewer for the web. It is currently in beta, so some irregularities are expexted. Also you should make sure you have a fast internet connection.

omero_fpbioimage_contextual-menu 

OMERO.figures

Maybe some of you already noticed, we got a little addition to our OMERO server. It is an additional web application (thus not available from the desktop client), that allows to produce figures from your images.  Bellow are some screenshots that give an idea how it looks like:

omero-web_figure-app

omero-figure_ui-screenshot

OMERO.figure is tailored for microscopy images and has the functionality to quickly produce a pdf-figure and does not clutter the interface with anything unnecessary.

Happy publishing!

New IT Infrastructure Launch

We would like to invite you to the launch presentation for the platform’s new IT infrastructure next Wednesday April 1st at 12:15. No joke.
The presentation will take place in the large Auditorium 0.110 Auditorium in Plant Biology.

We will talk about some new acquisitions the Bioimage Light Microscopy Facility has made recently that should help you with the management and the processing of your microscopy data.
Firstly and most importantly there is a new web-client for the batch processing of deconvolution jobs, the Huygens Remote Manager (HRM). We’ll demonstrate how this piece of software can be integrated easily in your workflow to improve the quality of your measurements from confocal microscopes. Secondly we’ll to give you a preview of OMERO. We are currently  in the middle of the final testing and would like to give you a glimpse of what is about to come. Finally we’ve just got the new licenses for Imaris 8. This might also be an opportunity to speak about the future requirements of the functionality and license numbers of this software.

SVI_huygens_presentation_smaller omero_web-client-screenshot