FalseColor-Python

A rapid digital staining module designed for translating two-channel fluorescence images (i.e. a nuclear and cytoplasmic stain) to the traditional H&E histopathology color space. Virtual H&E coloring methods based on: Giacomelli et al.

Full methods described in: R. Serafin et al.

Installation

In order to use FalseColor Python's GPU acceleration install cudatoolkit using conda:

conda install cudatoolkit

FalseColor Python can be installed using pip:

pip install falsecolor

Or by running setup.py install while in the working directory.

python setup.py install

Usage

See Examples to get started.

Several methods within color.py are setup with GPU acceleration using numba.cuda.jit: (See Example/GPU examples.ipynb)

#Set color levels for false coloring using background subtraction

import falseColor.coloring as fc
#Using Defaults:
settings_dict = fc.getColorSettings(key = 'HE')
nuclei_RGBsettings = settings_dict['nuclei']
cyto_RGBsettings = settings_dict['cyto']

#Or Levels can be set manually, provided they are in the following order
nuclei_RGBsettings = [R,G,B] # list of floats (0.0:1.0) for color levels in nuclear channel
cyto_RGBsettings = [R,G,B] # list of floats (0.0:1.0) for color levels in cyto channel

#nuclei,cyto are 2D numpy arrays for false coloring see GPU example.ipynb for more details
pseudo_colored_data = fc.rapidFalseColor(nuclei,cyto,
                                         nuclei_RGBsettings,cyto_RGBsettings)

Contributing

Pull requests are welcome. For major changes, please open an issue first to discuss what you would like to change.

License

GNU Affero General Public License v3.0

Copyright (c) 2019 Rob Serafin, Liu Lab, The University of Washington Department of Mechanical Engineering

License: GPL

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License 2 as published by the Free Software Foundation.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.