WORKSHOPS

NO SPACES AVAIL.ABLE

The workshop will cover an introduction to FRET, SRRF, spectral unmixing and deconvolution in the morning session. The afternoon will be an introduction to Leica SP5, How to measure a point spread function, How to acquire and process spectral images, Blind deconvolution, Spectral unmixing with reference spectra vs blind unmixing, Super-resolution by SRRF demo by Coherent Scientific. FRET demo.

Limited to 6 persons – participants are encouraged to bring a sample to test – please check with the workshop organiser for excitation wavelengths available and provide details on your test specimen. Sorry we can’t deal with PC2 samples in our lab unless they are fixed and dead. 

Transport from Hamilton is included in this workshop cost.

EBSD has become a well-established technique for microstructural characterisation in the SEM or FIB. The crystallographic data obtained can be used in the measurement of crystal orientation, misorientation, grain size distribution, texture, strain analysis, recrystallised / deformed fractions and grain boundary characterisation. The technique is used in a broad span of applications in many fields including metals & materials analysis and processing, microelectronics and earth sciences.

More recent developments in SEM-based diffraction have led to the technique of transmission kikuchi diffraction (TKD) which overcomes some of the resolution limitations of conventional EBSD enabling characterisation of materials at the nanoscale.

This one day workshop is an introduction to EBSD & TKD and will cover the following topics:

• The basic physics and how an EBSD system works
• What information can we get from EBSD and what kind of experiments can be performed 
• Hardware, calibration and tips for setting up the SEM for EBSD and TKD
• Sample preparation and why it is important
• Data presentation and analysis
• The benefits of combined EDS and EBSD
• Applications of EBSD and TKD

The Open Microscopy Environment (OME) is an open-source software project that develops tools that enable access, analysis, visualization, sharing and publication of biological image data. OME supports more than 150 image data formats across many imaging modalities including fluorescence microscopy, high-content screening, whole-slide imaging and biomedical imaging.

OME supports and visualizes multi-channel 3D timelapse images. OMERO is an open source, enterprise software platform developed by OME for image data management and analysis. OMERO is used in 1000s of institutions worldwide managing, sharing, analysing and publishing imaging datasets.

This workshop will cover all of the main functions of OMERO. We will demonstrate data import, organisation, viewing, searching, annotation and publishing. After we cover the basics of OMERO, we will demonstrate manual data processing and automated processing workflows using a range of open source applications running alongside OMERO. We will demonstrate how to integrate a variety of processing tools with OMERO such as ImageJ/Fiji, R and CellProfiler and how to programmatically generate output ready for publication.

This workshop is designed for researchers at all levels who work with data from digital microscopes or other imaging systems. The workshop includes presentations and hands-on session. Prior knowledge in microscopy, scripting and data analysis is not required.

Any student/researcher dealing with scientific images is more than welcome to join this workshop.

Have a plan of attack, it saves grief later on; consider your options, fancy might be tempting, but simple has its attractions too; and if thresholding has driven you to distraction, then the basics of machine learning might be the image analysis yoga-mat for you.

Image analysis isn’t a process to be done in isolation, irrespective of which method is chosen. Simply having a great method to extract information from an image is pointless if the image has been taken, selected, or processed in the wrong way. Numbers can lie.

This workshop probably won’t give you a customised method to analyse your images on the day, but it should give you the tools to think through an appropriate method to give accurate and reliable results when you return to your own comfortable lab.

The tools of choice will be Fiji (ImageJ) for general analysis techniques and using it in conjunction with Ilastik for the fabulous world of machine learning. Some overview will also be made of 3DSlicer, which is useful for 3D volumes, meshes, 3D alignments and suchlike. All are open source and run on Linux, OS X and Windows.