Zeiss CZI Import

Overview

Imports Zeiss CZI multidimensional microscopy data using Bio-Formats.

Requires bfGetReader() and bfGetPlane() from the Bio-Formats bfmatlab package.

IDCubePro imports the first time point only.

All channel and Z-slice combinations are converted into the third The third dimension is stored as sequential plane indices rather than being assumed to represent wavelength.

CZI X, Y, Z, C, and T dimensions, plane labels, and OME metadata summary are preserved when available.

Workflow

1. IDCubePro reads the first time point.

2. Channels and Z positions are converted into one plane stack.

3. Use plane labels to interpret each imported third-dimension position.

Plane index should not automatically be interpreted as wavelength.