BioFormatsVirtualLoader

class io.loaders.BioFormatsVirtualLoader

Bases: handle

BIOFORMATSVIRTUALLOADER - On-demand plane reader for MIB3 BioFormats virtual datasets.

Wraps a single microscopy file accessible via the Bio-Formats library. A loci.formats.Memoizer reader is opened lazily on the first readPlane call and kept open for the lifetime of the loader, avoiding the overhead of re-opening the reader for every z-slice and time-point.

Call close() (or let closeVirtualDataset delete the loader) to release the file handle when the virtual dataset is closed.

Unlike the batch loaders in +io/+loaders/ this class does NOT implement BaseImageLoader - it is stateful and designed for repeated single-plane reads rather than single full-dataset loads.

Usage example:

loader = io.loaders.BioFormatsVirtualLoader('/data/stack.czi', 0, tempdir);
planes = loader.readPlane([1 512], [1 512], 5, [1 2], 0, 'uint16');
% planes is [512, 512, 2] - one tile per requested channel
loader.close();
Constructor Summary
BioFormatsVirtualLoader(filename, seriesIndex, memoDir)

BIOFORMATSVIRTUALLOADER - Create an on-demand Bio-Formats plane reader.

Syntax:
obj = BioFormatsVirtualLoader(filename, seriesIndex, memoDir)
Input Arguments:

  • filename - [char] full path to the BioFormats-readable file

  • seriesIndex - [numeric] 0-based series index

  • memoDir - [char] directory for BioFormats Memoizer memo files

Output Arguments:

  • obj - [BioFormatsVirtualLoader] new loader instance

Property Summary
filename
memoDir

[numeric] 0-based series index (Virtual.seriesName{fileIdx} - 1)

reader

[char] directory for the BioFormats Memoizer memo files

seriesIndex

[char] full path to the BioFormats-readable file

Method Summary
close()

CLOSE - Close the Bio-Formats reader and release the file handle.

Syntax:
obj.close()

Safe to call multiple times.

delete()

DELETE - Destructor - closes the Bio-Formats reader when the object is destroyed.

Syntax:
obj.delete()
readPlane(Ylim, Xlim, planeId, colChannel, timepoint, dataClass)

READPLANE - Read one XY tile across the requested colour channels from a single z/t plane.

Syntax:
planes = obj.readPlane(Ylim, Xlim, planeId, colChannel, timepoint, dataClass)

The Bio-Formats reader is opened on the first call and reused on all subsequent calls to this loader.

Input Arguments:

  • Ylim - [1x2 numeric] pixel row range [ymin ymax] (1-based, inclusive)

  • Xlim - [1x2 numeric] pixel column range [xmin xmax] (1-based, inclusive)

  • planeId - [numeric] 1-based z-plane index within this file/series

  • colChannel - [1 x nC numeric] vector of 1-based colour channel indices

  • timepoint - [numeric] 0-based time-point index (as used by getIndex)

  • dataClass - [char] output class, e.g. 'uint8' or 'uint16'

Output Arguments:

  • planes - [nY x nX x nC numeric] array - one slice per requested channel