README.md

Installation

Install the required packages with:

pip install -r Requirements.txt

To install this as package make a local copy, activate your environment and run pip install:

>> git clone https://github.com/Zimmer-lab/imutils
>> conda activate my_env
>> pip install /path/to/folder/with/setup/dot/py

you can check https://github.com/Zimmer-lab/protocols/blob/master/computational/zimmer_lab_code_pipeline/04-installing_personal_python_packages.md for details.

Description

General:

This package has some image processing tools written by Ulises.

LoguruConfigurator:

A simple to use logging library. See documentation (docs)

Read Microscopy (Micromanager) dataset:

Open Dataset:

>> from imutils import MicroscopeDataReader
>> my_dataset = MicroscopeDataReader(dataset_path)

Get Data as lazy loaded dask array:

>> dask_array = my_dataset.dask_array
>> my_dataset.get_axis_order() > ['position', 'time', 'channel', 'z', 'y', 'x']
>> my_dataset.get_axis_string() > PTCZYX

Get single image as nparry (loaded into memory)

# image = my_dataset.read_image(position = position, time = time, channel=channel, z=z)
# (or get_frame)
>> image = my_dataset.get_frame(time = 42) # not given arguments are 0

View dataset with napari

# napari is not in the requirement file! Please install separately.
>> my_dataset.open_in_napari()

Additional Documentation

Additional Documentation as jupyter lab book in docs!

Write Microscopy (ndtiff) dataset:

Generate Dataset:

>> from imutils import MicroscopeDataWriter
>> my_dataset = MicroscopeDataWriter(dataset_path, dataset_name)

Write Image with coordinates ('position', 'time', 'channel', 'z', 'y', 'x' , 'stage_xyz_pos')

>> my_dataset.put_image(image=pixels, time=t)

Finish or Close dataset

>> my_dataset.close()

Additional Documentation

Additional Documentation as jupyter lab book in docs!