Code reference

This section does not cover the base classes, methods, and constants of qpimage, which can be found here.

module level aliases

For user convenience, the following objects are available at the module level.

class flimage.FLImage

alias of flimage.core.FLImage

class flimage.FLSeries

alias of flimage.series.FLSeries

flimage.META_KEYS_FL

alias of flimage.meta.META_KEYS_FL

core (FLImage)

Classes

class flimage.core.FLImage(data=None, meta_data={}, h5file=None, h5mode='a', h5dtype='float32')[source]

Fluorescence image manipulation

This class makes available fluorescence microscopy data in a manner similar to qpimage.QPImage.

Parameters
  • data (2d ndarray (float or complex) or list) – The experimental fluorescence image.

  • meta_data (dict) – Meta data associated with the input data. see flimage.meta.META_KEYS

  • h5file (str, pathlib.Path, h5py.Group, h5py.File, or None) – A path to an hdf5 data file where all data is cached. If set to None (default), all data will be handled in memory using the “core” driver of the h5py’s h5py:File class. If the file does not exist, it is created. If the file already exists, it is opened with the file mode defined by hdf5_mode. If this is an instance of h5py.Group or h5py.File, then this will be used to internally store all data.

  • h5mode (str) –

    Valid file modes are (only applies if h5file is a path)

    • ”r”: Readonly, file must exist

    • ”r+”: Read/write, file must exist

    • ”w”: Create file, truncate if exists

    • ”w-” or “x”: Create file, fail if exists

    • ”a”: Read/write if exists, create otherwise (default)

  • h5dtype (str) – The datatype in which to store the image data. The default is “float32” which is sufficient for 2D image analysis and consumes only half the disk space of the numpy default “float64”.

property bg_fl

background fluorescence image

property fl

background-corrected fluorescence image

property dtype

dtype of the fluorescence data array

property info

list of tuples with FLImage meta data

property meta

dictionary with imaging meta data

property raw_fl

raw fluorescence image

property shape

size of image dimensions

copy(h5file=None)[source]

Create a copy of the current instance

This is done by recursively copying the underlying hdf5 data.

Parameters

h5file (str, h5py.File, h5py.Group, or None) – see FLImage.__init__

set_bg_data(bg_data)[source]

Set background fluorescence data

Parameters

bg_data (2d ndarray, FLImage, or None) – The background data (must be same type as data). If set to None, the background data is reset.

image_data (basic image management)

Classes

class flimage.image_data.Fluorescence(h5, h5dtype='float32')[source]

Bases: qpimage.image_data.Phase

Dedicated class for fluorescence data

For fluorescence data, background correction is defined by subtracting the background image from the raw image.

Parameters
  • h5 (h5py.Group) – HDF5 group where all data is kept

  • h5dtype (str) – The datatype in which to store the image data. The default is “float32” which is sufficient for 2D image analysis and consumes only half the disk space of the numpy default “float64”.

meta (definitions for FLImage meta data)

Constants

flimage.meta.META_KEYS_FL = ['pixel size', 'time', 'flimage version', 'identifier', 'qpimage version', 'sim center', 'sim model', 'sim radius']

valid flimage.core.FLImage meta data keys

series (FLSeries)

Classes

class flimage.series.FLSeries(flimage_list=[], meta_data={}, h5file=None, h5mode='a', identifier=None)[source]

Fluorescence microscopy series data

Parameters
  • flimage_list (list) – A list of instances of flimage.FLImage.

  • meta_data (dict) – Meta data associated with the input data (see flimage.META_KEYS). This overrides the meta data of the FLImages in flimage_list and, if h5file is given and h5mode is not “r”, overrides the meta data in h5file.

  • h5file (str, h5py.Group, h5py.File, or None) – A path to an hdf5 data file where all data is cached. If set to None (default), all data will be handled in memory using the “core” driver of the h5py’s h5py:File class. If the file does not exist, it is created. If the file already exists, it is opened with the file mode defined by hdf5_mode. If this is an instance of h5py.Group or h5py.File, then this will be used to internally store all data. If h5file is given and flimage_list is not empty, all FLImages in flimage_list are appended to h5file in the given order.

  • h5mode (str) –

    Valid file modes are (only applies if h5file is a path):

    • ”r”: Readonly, file must exist

    • ”r+”: Read/write, file must exist

    • ”w”: Create file, truncate if exists

    • ”w-” or “x”: Create file, fail if exists

    • ”a”: Read/write if exists, create otherwise (default)

property identifier

unique identifier of the series

add_flimage(fli, identifier=None)[source]

Add a FLImage instance to the FLSeries

Parameters
  • fli (flimage.FLImage) – The FLImage that is added to the series

  • identifier (str) – Identifier key for fli

bleach_correction(h5out=None, border_px=20, flscorr=None, count=None, max_count=None)[source]

Perform a correction for photobleaching

Bleaching is modeled with an exponential and an offset.

Parameters
  • h5out (path or h5py.Group) – A new FLSeries will be written to this HDF5 file or h5py group.

  • border_px (int) – Number of border pixels to include for background estimation.

  • flscorr (flimage.series.FLSeries) – Apply the background correction to this FLSeries instead of the current instance. Use this in combination with filtered versions of the same series.

Returns

  • bg (float) – Background value subtracted from each image

  • flint (1d ndarray) – Fluorescence intensity trace extracted from the series

  • decay (1d ndarray) – Exponential fit to flint

  • times (1d ndarray) – Recording times corresponding to the indices in flint and decay

Notes

It is recommended to first denoise the fluorescence data with FLSeries.denoise do avoid an amplification of the background noise.

denoise(h5file, count=None, max_count=None)[source]

Denoise fluorescence data

h5file specifies a path or HDF5 group for the FLSeries to which the denoised fluorescence data is written.

get_flimage(index)[source]

Return a single FLImage of the series

Parameters

index (int or str) – Index or identifier of the FLImage

Notes

Instead of fls.get_flimage(index), it is possible to use the short-hand fls[index].