Convert Module API

napari_flim_phasor_plotter.convert.convert_folder_to_ome_tif(folder_path, x_pixel_size=0, y_pixel_size=0, z_pixel_size=0, pixel_size_unit='um', time_resolution_per_slice=0, time_unit='s', micro_time_resolution=0, micro_time_unit='ps', channel_names='', number_channels='0', cancel_button=False)

Convert a folder of FLIM images representing an image stack to OME-TIFF files.

Parameters

folder_pathpathlib.Path

Path to the folder containing the FLIM images.

x_pixel_sizefloat, optional

Pixel size along the x-axis, by default 0.

y_pixel_sizefloat, optional

Pixel size along the y-axis, by default 0.

z_pixel_sizefloat, optional

Pixel size along the z-axis, by default 0.

pixel_size_unitstr, optional

Unit of the pixel size, by default ‘um’.

time_resolution_per_slicefloat, optional

Time resolution per slice, by default 0.

time_unitstr, optional

Unit of the time resolution, by default ‘s’.

micro_time_resolutionfloat, optional

Time resolution for the TCSPC histogram, by default 0.

micro_time_unitstr, optional

Unit of the time resolution for the TCSPC histogram, by default ‘ps’.

channel_namesstr, optional

Names of the channels, separated by comma, by default ‘’.

number_channelsstr, optional

Number of channels, by default 0. Not used, but required for the widget and filled from the metadata.

cancel_buttonbool, optional

Cancel button for the widget, by default False.

Returns

None

napari_flim_phasor_plotter.convert.convert_file_to_ome_tif(file_path, x_pixel_size=0, y_pixel_size=0, pixel_size_unit='um', micro_time_resolution=0, micro_time_unit='ps', channel_names='', number_channels='0', cancel_button=False)

Convert a single FLIM file to an OME-TIFF file.

Parameters

file_pathpathlib.Path

Path to the FLIM image file.

x_pixel_sizefloat, optional

Pixel size along the x-axis, by default 0.

y_pixel_sizefloat, optional

Pixel size along the y-axis, by default 0.

pixel_size_unitstr, optional

Unit of the pixel size, by default ‘um’.

micro_time_resolutionfloat, optional

Time resolution for the TCSPC histogram, by default 0.

micro_time_unitstr, optional

Unit of the time resolution for the TCSPC histogram, by default ‘ps’.

channel_namesstr, optional

Names of the channels, separated by comma, by default ‘’.

number_channelsstr, optional

Number of channels, by default 0. Not used, but required for the widget and filled from the metadata.

cancel_buttonbool, optional

Cancel button for the widget, by default False.

Returns

None

napari_flim_phasor_plotter.convert.convert_folder_to_zarr(folder_path)

Convert a folder of FLIM images to a zarr file.

The folder must contain only FLIM images of the same type (e.g. all .ptu files or all .sdt files). The file names must be in the format: “name_t000_z000” where “t000” is the time point and “z000” is the z slice. The z slice and time point must be the last two numbers in the file name. The z slice and time point must be separated by an underscore.

Parameters

folder_pathstr

Path to the folder containing the FLIM images.

Returns

None