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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.

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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 

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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Huygens Workshop

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This autumn the makers of the Huygens Software will give a workshop about image deconvolution at the University of Fribourg.
There is no perfect instrument, every device comes with a certain number of imperfections, that impact our measurements. This is also true for light microscopy, where we encounter spherical aberrations, chromatic aberrations, bleaching, stage drift, and diffraction related distortions (blur) among an even wider spectrum of phenomena, that can have some undesired impact on image acquisition.
This workshop will be all about how to deal with this kind of measurement imperfections and what the experimenters can do about it.  To situate this techniques also referred to as image restoration see the figure bellow, putting image restoration into the context of a typical biomedical experiment pipeline.

experiment-pipeline

This workshop is of particular interest to researchers, that want to study small, sub-cellular structures by the means of three-dimensional epi-fluorescence microscopy. Image restoration can significantly improve the quality of acquired images, rendering small structures like axons more distinguishable and allow for a more reliable object quantification.

Organisation

date: 15. September 2017 from 9:00-17:00
location: PER21, F230
participation conditions: UniFr staff, free of charge, registration required

Participants are free to attend only the theoretical part in the morning (about the why and the how of deconvolution) or  the entire workshop with a practical session in the afternoon.

Schedule

Time Description
 09:00-10:30 presentation of Huygens (functionality, use cases)
 10:30-10:45   coffee break
 11:00-13:00 deconvolution theory: experimental design, sampling, pitfalls, etc. (includes hands-on examples)
13:00-14:00   lunch break
14:00-15:15 Introduction to Huygens Remote Manager
15:00-16:00 Work on your own data

Registration

Registration is closed.

Imaris Workshop 4. July 2017

imaris-track-example imaris-filament-example

For friends of 3D image processing and analysis:  We are happy to announce the next Imaris workshop here in Fribourg. This is an opportunity to get the overview of the latest functionality of the software and to either familiarize with tutorials or start to work on a solution for your own data.

Find all the details on the event page. The workshop is free for all facility users. Please register (login required) rather early than too late, there is only a limited number of slots available.

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

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:

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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