pyoformats 1.1.3

PyoFormats: Simple wrapper for python-bioformats

PyoFormats

Simple wrapper for python-formats

Example

from pyoformats import read

# start JVM
read.JVM().start()

# displays names and shapes of all available series in file
read.file_info("test.msr")

# get series count of file
n_series = read.series_count("test.msr")

# returns 5d numpy array of image in series
my_image = read.image_5d("test.msr", series=1)

# read only certain z-slices. (Note, also channels and frames can be selected)
my_image = read.image_5d("test.msr", series=1, zslices=[2, 3, 5, 8, 13])

# get physical pixel sizes
xyz_sizes = read.pixel_sizes_xyz("test.msr", series=0)

# get physical pixel units
xyz_sizes = read.pixel_sizes_xyz_units("test.msr", series=0)

# iterate over all series and extract name and pixel data
for s, data in read.image_5d_iterator("test.msr"):
    print(s, data.shape)


# at end of script
read.JVM().shutdown()

Installation

Detailed How-To for installing dependencies (Windows/ MacOS)

Before you install the pyoformats Python package, check out detailed instructions for installing dependencies.

from PyPi

pip install pyoformats

pyoformats directly from gitlab

pip install git+https://git.ist.ac.at/csommer/pyoformats.git

or local

1. git clone https://git.ist.ac.at/csommer/pyoformats.git
2. cd pyoformats
3. pip install -e .

Dependencies

• numpy
• javabridge
• python-bioformats