Fiji and BigDataViewer

Owned by Ofra Golani
Last updated: Jul 12, 2016
2 min read

Fiji and Big DataViewer plugin can be used for Daa Visualization and Data Fusion 

The following resources provide very detailed usage information 

Reference Methods Paper which details all the steps:

BigDataViewer page on ImageJ website 

 

Lightsheet Data Visualization with BigDataViewer

 

Features: let you explore view arbitrary rotated slice through your data , very fast (if you save in hdf5 format)

Cons: don't have volume rendering , eg. MIP and blend/volumetric

 

Prepare: Upload dataset and save in hdf5 format

In the reference paper, follow the steps "Define Dataset" and "Resave Dataset in HDF5 Format"

 

Explore: The core functions of the BigDataViewer33 are explained in Table 2 and http://fiji.sc/BigDataViewer.http://fiji.sc/BigDataViewer.

 

DualSideFusion 

Follow steps (7. Multiview Fusion => "2. Content-based Multiview Fusion"     in the Reference paper

make sure to:

  1. select all time points you want to fuse
  2. save into new HDF5 file (first window)
  3. select "Content-based fusion" - it should be better (second window)
  4. select the output HDF5 file to be under your AnalyzedData folder ("Export path" in 3rd window)

 

Dual Side Fusion + Deconvolution - is also possible ....

 

Multi-View Fusion using beads and Multi-View Fusion are also described in the paper