Tag Archives: 3D-image-processing

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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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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.

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Imaris 9.3

Imaris 9.3 is available. Find out more about the software on the Bitplane website.

The first apparent change will be the end of the arena. Instead of its own database, there is now the possibility to add ‘observed’ folders to Imaris to facilitate the access to your ims-files.
The first time Imaris is launched, you will be prompted to use the migration assistant, that allows to extract existing images from the arena. You can find a short tutorial in this video.

You might also wonder look in vain for functionality like filtering or background subtraction under  Menu > Image Processing. Now instead there is a new icon in the toolbar:

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This will bring up the following window where you can chain together all the basic pre-processing operations together for the different channels of your dataset.

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The complete list of novelties can be found on the ‘what’s new‘ page. You might also be interested in the change-list in the release notes.

We installed this latest version on our number crunchers.

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Bioimage-Informatics Clinic

In 2018, effective immediately, we like to introduce the Bioimage-Informatic-Clinic.

This means that once a week our door is open for you to seek council for image and data analysis and general topics around microscopy data. Topics include: image restoration, deconvolution, volume reconstruction, image alignment (registration), 3D image processing, object segmentation, object tracking, object quantification, co-localisation analysis, batch processing, data visualisation, data analysis pipelines, data management and many more.

Every Tuesday afternoon from 13:00 – 17:00  you can bring your microscopy data (external HD or the server address) and your questions  to PER02 1.406.
Visitors will be attended to on a first come first served basis (no need to arrange a meeting). Come around, hang-out and let’s crunch some numbers.

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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.

Huygens Workshop 15. September 2017

You would like to get the best out of your image data, try to push the resolution? If this is the case you should sign up for the upcoming Huygens  workshop. During this one-day-workshop you can learn about image restoration and how you can apply it to your own image data here at the University of Fribourg.

Find all the details of the workshop on the event-page.

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Imaris Workshop

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At the University of Fribourg we use Imaris to process and analyse multidimensional image data-sets issue from epi-fluorescene microscopy.  In particular we use it’s advanced functionality for 3 dimensional (optically sectioned) image data and perform volumetric analysis.

We organise a worksop with representatives of Bitplane for you, to discover the possibilities of the software and train yourself as a user.

Further information:

Organisation

date: 4. July 2017 from 9:00-17:00
location: PER II, F230
participation conditions: UniFr staff, free of charge, registration required

Participants are free to only attend the presentation of Imaris or to work through the entire workshop.

schedule

Time Description
 09:00-10:30 presentation of Imaris (functionality, use cases)
 10:30-10:45   coffee break
 11:00-13:00 introduction to Imaris (basics)
13:00-14:00   lunch break
14:00-15:30 hands-on workshop
15:30-16:00   coffee break
16:00-17:30 hands-on workshop

 

Registration

… is closed