Tag Archives: hardware

NZ-S60_FSP-pic

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.

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