This repo provides code for lightsheet imaging data analysis pipeline for extraction of quantitative readouts regarding vascular volume and drug penetration in tumors.
A custom data analysis pipeline was developed to enable rapid analysis of tumor lightsheet datasets. Key goals of this analysis pipeline are:
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Enable extraction of quantitative readouts regarding drug penetration in whole tumors from lightsheet data sets. See Dobosz et al. 2014., Neoplasia1 for reference.
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Use python programming to make use of open source packages that can support building a custom pipeline.
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Use cloud computing environment (Merck High Performance Computing Resources) to enable rapid analysis of very large lightsheet data sets.
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Develop an analysis pipeline with two run modes:
a) Automatic run mode: enables executing full analysis pipeline on a new data set via a single line of code
b) Lego Brick mode: enables re-using parts of the analysis pipeline for building new analysis methods.
The code documentation and examples may be found here
Title:
A Light sheet fluorescence microscopy and machine learning-based approach to investigate drug and biomarker distribution in whole organs and tumors.
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Authors:
Niyanta Kumar, Petr Hrobař, Martin Vagenknecht, Jindrich Soukup, Nadia Patterson, Peter Bloomingdale, Tomoko Freshwater, Sophia Bardehle, Roman Peter, Ruban Mangadu, Cinthia V. Pastuskovas, and Mark T. Cancilla
Merck & Co., Inc.
In case of need of any editional (technical) information reach out to the development team via github's issue:
- Martin Vagenknech (Merck & Co., Inc.)
- Petr Hrobar (Merck & Co., Inc.)
- Jindrich Soukup (Merck & Co., Inc.)
Repo is a python package. Installation process can be automated via bash .sh
file in the environment_setup
folder.
Clone the github repository (Entire project in one folder) by running:
# Clone The repo localy to your computer
git clone https://github.com/Merck/3D_Tumor_Lightsheet_Analysis_Pipeline.git
# Navigate to the repo folder
cd 3D_Tumor_Lightsheet_Analysis_Pipeline
When installing the package:
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MAC/LINUX Users
2.1) Make sure you have conda installed on your computer. if not, you may use this link.
2.2) Create a python environment
Run in the terminal:source environment_setup/set_3d_infrastructure.sh
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Windows Users
2.1) Make sure you have conda installed on your computer. if not, you may use this link.
2.2) Create a python environment run all lines of
environment_setup/set_3d_infrastructure.sh
manually in the terminal
To operate the code on local computers we recommend the following MINIMAL Hardware Requirements:
- CPU with at least 6 Cores
- 16 GB RAM
- 800 GB Storage for the Data
- GPU is only required when deep learning model (UNET) is being used.
Copyright © 2022 Merck & Co., Inc., Kenilworth, NJ, USA and its affiliates. All rights reserved.
Footnotes
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Dobosz, M., Ntziachristos, V., Scheuer, W. & Strobel, S. Multispectral Fluorescence Ultramicroscopy: Three-Dimensional Visualization and Automatic Quantification of Tumor Morphology, Drug Penetration, and Antiangiogenic Treatment Response. Neoplasia 16, 1-U24, doi:10.1593/neo.131848 (2014).* ↩