make_hyperstack: Read one or more TIFFs into 4D hyperstack

In jefferis/scanimage: read and analyse 2 photon images from ScanImage

Description

make_hyperstack reads a single TIFF which may have 3-4 dimensions.

make_hyperstack_multifile reads multiple TIFFs each of which will have 2-3 dimensions (usually x,y,t) and combines into a single hyperstack x,y,t,file

Usage

make_hyperstack(x, zslices, timepoints, time.axis = 4, ...)

make_hyperstack_multifile(x, file.axis = 4, ...)

Arguments

x	Path to (one or more) TIFFs
zslices	Number of zlices in each TIFF
timepoints	Number of timepoints in each TIFF
time.axis	Which axis will end up as the time axis in the output
...	Additional arguments passed to make_hyperstack, thence to read.any.tiff and eventually to read.scanimage.
file.axis	Which axis will end up as the file axis in the output when reading multiple files

Details

Where possible the hyperstack will include the description attribute from the original scanimage file. This can be used with scanimageinfo or parse_description to access useful information about the underlying image.

Value

a 4D array typically ordered x,y,z,t or x,y,t,file.

jefferis/scanimage documentation built on May 19, 2019, 3:58 a.m.