Other formats

PIMS

Through PIMS, MorphoCut supports reading Bioformats and Video.

PIMS is a lazy-loading interface to sequential data with numpy-like slicing.”

Note

PIMS is required to use the nodes defined in this module.

morphocut.pims.BioformatsReader(path, meta, series=None, **kwargs)[source]

Stream Read frames from Bio-Formats files.

Bio-Formats is a software tool for reading and writing image data using standardized, open formats. It is able to read over 150 file formats, including OME-TIFF and Amnis FlowSight (.cif).

Note

JPype is required to use this reader.

On first use of BioformatsReader, the required java library loci_tools.jar will be automatically downloaded from openmicroscopy.org.

Parameters
  • path (str) – Path to a Bioformats file.

  • meta (bool, optional) – When true, the metadata object is generated. Takes time to build.

  • series (int, optional) – Active image series index. Defaults to None, meaning that all series are read.

  • **kwargs – Additional keyword parameters for pims.BioformatsReader

Example

frame, series = BioformatsReader(path)

# frame (pims.Frame): The frame.
#   frame.frame_no (int): Frame number.
#   frame.metadata (dict): Frame metadata.
# series (int): The series extracted from the file.
morphocut.pims.VideoReader(path, **kwargs)[source]

Stream Read frames from video files.

Note

PyAV is required to use this reader.

Parameters
  • path – Path to a video file.

  • **kwargs – Additional keyword parameters for pims.PyAVReaderIndexed.

Example

frame = VideoReader(path)

# frame (pims.Frame): The frame.
#   frame.frame_no (int): Frame number.
#   frame.metadata (dict): Frame metadata.

Example

from morphocut import Pipeline
from morphocut.image import ImageWriter
from morphocut.pims import VideoReader
from morphocut.str import Format

with Pipeline() as p:
    frame = VideoReader("/path/to/video.avi")
    filename = Format("/output/path/frame_#{}.png", frame.frame_no)
    ImageWriter(filename, frame)

p.run()

Contributed

EcotaxaReader

Stream Read an archive of images and metadata that is importable to EcoTaxa.

EcotaxaWriter

Create an archive of images and metadata that is importable to EcoTaxa.