This is a (beta) version of a library that I wrote to import image files from the file structure created by Harmony and to further process them in a sequential or parallel way.

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Given that the Harmony software for the Operetta microscope has a rather obscure pipeline, which is also not open source, I've decided to write a pipeline on my own. The current version let's you import the files into a Python script, do image analysis and compile the results into a Pandas dataframe. Some tools for cell cycle gating and plotting utilities are still available, but will be removed soon to give this package a unique purpose.

PENDING!

Requires Python 3.6 or greater. There are also some packages that this library depends on. For specifics, see requirements.txt, but the main packages required are

• Pandas - version >0.23.4
• Scikit image - version >0.14.0
• Shapely - version >1.6.4
• Matplotlib - version >3.0.2
• Seaborn - version 0.9.0

git clone https://github.com/fabio-echegaray/operetta.git Then, on the working folder run: pip install -r requirements.txt

PENDING

Look at batch.py and position.py

List of features ready and TODOs for future development

• Importing and csv generation (powered by Pandas) of all the files in the Harmony file output.
• Parallel processing capable. HPC cluster script provided as an example.
• Cell Cycle gating feature (provided two DNA markers, ex. DAPI & EbU)
• Manual measurements of ring-like structures.
• Some plotting utilities.

To-do list:

• Improve processing pipeline.
• Move interactive applications to separate project.

Project is in progress. It still doesn't comply 100% with Harmony file format (would be grateful if anyone has more documentation of it), and working on better processing support.

Created by @fabioechegaray

• [email protected]
• github Feel free to contact me!

Image Processing in Python for PerkinElmer's Operetta Microscope
Copyright (C) 2020  Fabio Echegaray

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

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 Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.