tiftool 0.2.4

tiftool

tiftool: A Python package for Microscopy tif images

The package for dealing tif stack image. Oriented for Microscopy image, offering useful processing. Under construction, I'll make description site and more functions, maybe for 2020.08.

Concept

Stack object

Main concept of tiftool is Stack object. This object carries your 3d data from .tif file as 'torch.Tensor' or 'numpy.ndarray'. By using stack object, you can conduct numerous processes; MIP(Maximum Intensity Projection), Find center z-plane, etc. This package is made to help research, Fluorescent Microscopy(WideField, XLFM(eXtended field of view LFM), etc).

HyperStack object

Under construction Similar as ImageJ, I'll make HyperStack object which can consider 'time'. It will contain 4-D data, (T, X, Y, Z).

Installation

pip

tiftool can installed via pip. Simply run this code by terminal.

pip install tiftool

Latest version is 0.1.5. If you have older version of tiftool, run this code to update. I strongly recommend to use latest version.

pip install tiftool -U

Running tiftool

Basic things using stack object

import tiftool.stack as st

larva = st.Stack().open("larva.tif").to_tensor()  # Change to torch.tensor, default data is numpy array.
raw_data = larva._data  # You can access the raw data inside Stack() object.
print(raw_data.size())  # torch.size([1098, 890, 64]) (x, y, z)

MIP = larva.mip_3d()  # Return Maximum Intensity Project for x, y, z axis
MIP.show()  # Show image using matplotlib
MIP.write("mip_larva.tif")  # write at your input path

See tiftool docs for more details. (Not constructed)

Issues & Contribution

I appreciate for all issues and contributions. You can use 'issues' tab, 'Pull request' tab, or e-mail me! I want to develop this package as a powerful toolkit for microscopy data researcher and if you mind, contribute with me! :smiley:

LICENSE

This package follows MIT LICENSE.