The following table shows the available navigation commands using the mouse:
ims files select Plugins › BigDataViewer › Open Imaris (experimental) from the Fiji menu. Imaris (Bitplane) uses a hierarchical data format (similar to BigDataViewer’s XML/HDF5 format). Subsequently select Plugins › BigDataViewer › Open Current Image which will launch the BigDataViewer with the sample image, for navigation by arbitrary re-slicing. Since Fiji relies of LOCI Bioformats library that means essentially all know microscopy file formats.įor example, open the sample image File › Open Samples › Mitosis (26MB, 5D stack) from the Fiji menu. The BigDataViewer can be used to visualise and navigate any image that can be opened in Fiji. To start BigDataViewer, select Plugins › BigDataViewer › Open XML/HDF5 from the Fiji menu.
Download both the XML and the HDF5 file and place them somewhere next to each other.Īlternatively, you can create a dataset by exporting your own data as described below. This is an excerpt of a 6 angle 715 time-point sequence of drosophila melanogaster embryonal development, imaged with a Zeiss Lightsheet Z.1. You can download a small dataset from here, comprising two views and three time-points. Our custom XML/HDF5 is a special purpose hierarchical data format that optimises access to any part of large-multi view datasets using ImgLib2. There are various options: Multi-view data converted to XML/HDF5Ī special purpose of BigDataViewer is to visualise multi-view light sheet microscopy datasets. To use the BigDataViewer we need some example dataset to browse. You should have a sub-menu Plugins › BigDataViewer.
The XML file contains metadata, for example the registration of sources to the global coordinate system. Images are represented as tiled multi-resolution pyramids, and stored in HDF5 chunked multi-dimensional arrays. The file format is based on XML and HDF5. This permits browsing to any location within a multi-terabyte recording in a fraction of a second. In a multi-angle, multi-channel SPIM sequence, each channel of each angle is a source.īigDataViewer comes with a custom data format that is is optimized for fast random access to very large data sets.
For example, in a multi-angle SPIM sequence, each angle is a source. Each source provides one 3D image (for each time-point in the case of a time-lapse sequence). BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji’s SPIMage processing pipeline.Ĭonceptually, the visualized data comprises multiple data sources. The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences.
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