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Updated README
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hlgirard committed Sep 27, 2019
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Integrated tool to measure the nucleation rate of protein crystals from the crystallization kinetics of an array of independent identical droplets.

From a directory containing a time-series of images of mutliple droplets, the tool segments individual droplet and uses a pre-trained CNN model to determine the presence or absence of crystals in each drop.
From a directory containing a time-series of images of multiple droplets, the tool segments individual droplet and uses a pre-trained CNN model to determine the presence or absence of crystals in each drop.
The nucleation rate is evaluated from the rate of decay of the proportion of drops that _do not_ exhibit visible crystals.

![Schematic](docs/CrystalML_demo.jpg)
![Schematic](docs/crystalml_schem.jpg)

## Installation

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### Quickstart

A time series of images of an emulsion of protein-ladden droplets must be stored in a directory prior to usage of CrystalML
A time series of images of an emulsion of protein-laden droplets must be stored in a directory prior to usage of CrystalML
The application can then be used to process the images as follows:
```
crystalml process --save-plot path/to/directory
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#### Arguments

- `-c`, `--check-segmentation` displays the result of segmenting an image (selected at approximately 80% of the time series) to verify that the segementation algorithm works well before processing.
- `-c`, `--check-segmentation` displays the result of segmenting an image (selected at approximately 80% of the time series) to verify that the segmentation algorithm works well before processing.
- `-o`, `--save-overlay` resaves all images in the directory with an overlay showing detected droplets in red (no crystal) or green (crystal detected) for process control.
- `-p`, `--save-plot` generates and saves plots of crystal contents over time
- `-v`, `--verbose` increases the verbosity level
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- `-tb`, `--tensorboard` saves logs for tensorboard visualization in `<cwd>/logs`
- `-v`, `--verbose` increases the verbosity level

## Repository strutcture
## Repository structure

- `models`: pre-trained machine learning models for crystal presence discrimination
- `notebooks`: jupyer notebooks evaluating different image segmentation strategies
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