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Handling multi-dimensional images with SyncWindows and Image5D

Administrative Information


Till I.D. GmbH

Presentation Information

Full / Half Time Slot: Half Time Slot (25 min)

Contact / Speaker Name

Joachim Walter

Presentation Title

Handling multi-dimensional images with SyncWindows and Image5D

Participant Requirements

presentation for beginners

Biography of Speaker

Joachim Walter studied physics at the university of Heidelberg.
He did his PhD on live cell microscopy and DNA-repair in the group of Thomas Cremer at the LMU Munich.
Since 2002 he works for Till I.D. GmbH,Martinsried.


ImageJ by itself handles image data with up to three dimensions. That means that 3D image stacks or time series of 2D images can be viewed and processed. A number of plugins are available to handle image data with multiple color-channels, slices and/or time-points. Two of these tools are presented here in detail: SyncWindows and Image5D.
SyncWindows synchronizes cursor movements, mouse clicks and movement of the slice selector between selected images and image stacks. When images from multiple color-channels are synchronized, the same region of interest can be selected and measured in all channels. An extension of SyncWindows, SyncMeasure3D, allows simultaneous measuring of volumes and centers of hand-selected 3D-objects. It is also useful for measuring the shift between images of an object in different color channels (“chromatic shift”).
Image5D allows browsing of time series of multi-channel image-stacks. The color channels can be overlaid in selectable colors and quickly switched on and off. Existing plugins see and process the currently selected z-stack of an Image5D as a normal image-stack. Additionally, there are plugins to make projections and montages from all or selected channels of an Image5D.

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