Opening Raw FLIM Data

Opening Raw FLIM Data#

You can open raw fluorescence lifetime imaging microscopy (FLIM) data in napari by dragging and dropping compatible files (or folders with files for stacks) into the viewer.

opening_data

Input Data Types#

This plugin can read the following FLIM file types:

  • .ptu

  • .sdt

  • .tif (including ome.tif)

  • .zarr

This plugin works with the following data shapes:

  • 2D FLIM images (actually 3D data where FLIM counts are in the first axis, i.e., (photon_counts, y, x)).

  • 3D FLIM images (actually 4D data where FLIM counts are in the first axis, i.e., (photon_counts, z, y, x)).

  • 3D timelapse FLIM images (actually 5D data where FLIM counts are in the first axis, i.e., (photon_counts, t, z, y, x)).

  • Multichannel .tif or .zarr data may need to be loaded separately.

If you read your files using this plugin as a reader, it returns and works with the data axes in the following order (data from multiple detectors are displayed as distinct napari layers):

(photon_counts, time, z, y, x)

Even if the data is 2D, the plugin will add a unitary time and a z axis. It also provides the standard intensity image in another layer by summing the photon_counts dimension.

Opening a Raw FLIM Image#

Drag and drop a compatible file format (check supported file formats above) to open a FLIM image. It gets displayed in two layer: a ‘raw FLIM image series’ (a sequence of intensity images each corresponding to an individual time point of the FLIM ‘micro-time’), and a timely summed up image (usually just known as the ‘intensity’ image). Scrolling through the FLIM time series provides a first glimpse of lifetimes across image regions.

Loading Stacks#

If you have multiple slices or time-points as separated files, you can choose a folder containing the files. In order for the plugin to properly build a stack, the file names must contain some indication about which slice or time-point they represent, i.e., each file name should contain a _t and/or _z followed by a number.

Here are a few example templates:

  • timelapse:

    • image_t001.ptu

    • image_t002.ptu

  • z-stack:

    • image_z01.sdt

    • image_z02.sdt

  • 3D timelapse:

    • image_t001_z001.tif

    • image_t001_z002.tif

    • …

    • image_t002_z001.tif

Sample Data#

The plugin comes with a few sample FLIM raw images:

  • ‘2D’ raw FLIM images:

    • Hazelnut (originally a .ptu file)

    • Seminal Receptacle (originally a .sdt file)

  • ‘3D’ raw FLIM image stack (Hazelnut 3D)

    • Hazelnut 3D (originally a series of .ptu files)

  • ‘2D’ synthetic FLIM image

    • Lifetime Cat

To load it, go to File > Open Sample -> FLIM phasor plotter.

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