Array Tomography

Setting up for reading ets files (from Olympus scope)

The reader is based on the maltab project imreadBF. All the required files, including the java class are under loacated in /external/imreadBioFormat.

One needs to add the loci_tools.jar class file to Matlab.

edit class

then add at the bottom the path to [full path to PBlabToolkit]/PBlabToolkit/external/imreadBioFormat

Also add the imreadBioFormat directory to your Matlab path and make.

Finally restart Matlab and the BioFormat reader should be ready.

Collecting ets files from an Olympus CellCens imaging session into a stack (one stack per channel).

This step depends on the way the ets file was generated and its content (how many planes, time points etc) so the script gatherStackFromMultiEtsFiles.m is provided as an example.