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Paper and Readme update
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Oftatkofta committed Aug 14, 2020
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16 changes: 11 additions & 5 deletions paper.md
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Expand Up @@ -9,7 +9,7 @@ authors:
- name: Jens Eriksson^[Corresponding author]
orcid: 0000-0002-8945-2665
affiliation: 1
- name: Daniell Styrström
- name: Daniel Styrström
affiliation: 2
- name: Mikael Sellin
orcid: 0000-0002-8355-0803
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# Summary

Studying the coordinated movement of confluent cells can give insigths in to may different biological phenomena, such as wound healing, cancer metastasis, and host responses to bacterial infections. Such experiments can collectively be termend as confluent cell dynamics. Confluent cell dynamics is most often investigated by analyzing time lapse images generated by live cell microscopy. Thanks to recent developments in cell biology it is now possible to genereate tissue-like arrangements of primary cells, aslo known as organotypic culture. However, one disadvantage of such systems is that
Studying the coordinated movement of confluent cells can give insigths in to may different biological phenomena, such as wound healing, cancer metastasis, and host responses to bacterial infections. Such experiments can collectively be termend as confluent cell dynamics. Confluent cell dynamics is most often investigated by analyzing time lapse images generated by live cell microscopy. Thanks to recent developments in cell biology it is now possible to genereate tissue-like arrangements of primary cells, aslo known as organotypic culture or organoids. However, one disadvantage of such systems is that it is currently very laboursome to generate fluorescently labeled live samples, which makes optical flow based analysis of bright field (black and white) microscopy images the primary method to extract information from these systems.

Analyzing brightfield microscopy time lapse images in order to study collective cell dynamics


# Statement of need

Cellocity is an bioimage analysis tool for quantifying confluent cell dynamics written in Python. It has been developed to be a "one-stop-shop" for researchers interested in investigating cell dynamics. Cellocity allows the user to test different analysis algorithms, such as PIV and optical flow, and visualizations where crucial image metadata is always retained

# Statement of need

Cellocity is an bioimage analysis tool for quantifying confluent cell dynamics written in Python. The main advantages of Cellocity is its ability work on unlabeled Brightfield time lapse microscopy data, and its ability to both quantify and visualize abstract optical flow analysis to the user. Cellocity aims to make optical flow based analysis of microscopy data easier by providing a framework that keeps track of image metadata, performs common pre-processing steps, and implements previously published analysis algotithms. The architecture of Cellocity is designed to be highly customizable and modular. Implementing new analysis modules, image readers, and visualizations is straight forward with the help of Cellocity's developer guide and API.
The main advantages of Cellocity is its ability work on unlabeled Brightfield time lapse microscopy data, and its ability to both quantify and visualize abstract optical flow analysis to the user. Cellocity aims to make optical flow based analysis of microscopy data easier by providing a framework that keeps track of image metadata, performs common pre-processing steps, and implements previously published analysis algotithms. The architecture of Cellocity is designed to be highly customizable and modular. Implementing new analysis modules, image readers, and visualizations is straight forward with the help of Cellocity's developer guide and API.

# Acknowledgements

We acknoledge the contribution of Pilar Samperio Ventayol who prepared the fixed murine epithelium monolayer used for generating the validation dataset.

# References
7 changes: 5 additions & 2 deletions readme.md
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# Cellocity

Cellocity is a python package that allows the user to perform optical flow and PIV analysis on microscopy data.

# Velocity and vector analysis of microscopy data
## Velocity and vector analysis of microscopy data

# Documentation
Cellocity can create vector field visualizations, speed graphs, and multiple advanced vector field analysis.

## Documentation

Documentation is available at [Read the Docs](https://cellocity.readthedocs.io/en/latest/).

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