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 is a :rocket:, 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 0.2.1. If you have older version of tiftool, run this code to update. I strongly recommend to use latest version.
pip install tiftool -U
not recommended If you want to force ignore all dependencies, you can use –no-dependencies switch of pip stackoverflow.
pip install --no-dependencies tiftool
tiftool might not work well if your environment doesn’t have requirements…
wheel
If upper method does not work, you can install tiftool via wheel(.whl) file. Install wheel from this .whl link.
pip install yourpath/...whl
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.