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Adding workshop material for v1 release
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.gitignore

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.DS_Store
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.vscode
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.ipynb_checkpoints/
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.aws-sam/

README.md

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## My Project
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# Biological Cell Segmentation using Amazon SageMaker
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TODO: Fill this README out!
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> Please see the AWS Workshop for a complete end-to-end tutorial on using this repository. https://catalog.us-east-1.prod.workshops.aws/workshops/7fb985db-2c2c-4f72-8aa6-7a1c8202b61a
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Be sure to:
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This workshop outlines a machine-learning cell segmentation architecture from scratch for the life-sciences vertical. The use-case is tailored towards having a particular cell of interest from the lab (e.g human embryos, hepatocytes cells, etc) and wish to determine the number of cells, density and basic characteristics of the sample from a microscopy image.
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* Change the title in this README
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* Edit your repository description on GitHub
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The workshop is expected to take *3 hours*, aimed at individuals who want to learn how Machine Learning can help make predications based on open data. No specific background knowledge is required. The workshop provides step-by-step instructions along with the code required to run each step to cover the following:
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* Downloading the dataset from the Broad Bioimage Benchmark Collection (BBBC005) which will be used for training purposes to build our model.
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* Demonstrate the process to use a SageMaker Notebook to train a model form scratch, specifically for cell-segmentation.
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* Setting up an SageMaker Inference endpoint to host our model.
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* Configuring S3 with event notifications, which will trigger a Lambda function which will invoke our SageMaker inference endpoint for processing an image to determine the cell segmentation.
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The aim of the workshop is to introduce building a model from scratch and how to use Amazon SageMaker to train and host a model, using a serverless architecture for processing images uploaded to an S3 bucket which interface with a SageMaker inference endpoint.
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## Training architecture
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The architecture for training the model consists of the following:
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![Training](/static/training.png)
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## Inference architecture
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The architecture for running inference consists of the following:
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![Inference](/static/inference-v1.png)
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## Next steps
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Please see the AWS Workshop for a complete tutorial on using this repository.
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https://catalog.us-east-1.prod.workshops.aws/workshops/7fb985db-2c2c-4f72-8aa6-7a1c8202b61a
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## Security
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See [CONTRIBUTING](CONTRIBUTING.md#security-issue-notifications) for more information.
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## License
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This library is licensed under the MIT-0 License. See the LICENSE file.
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This library is licensed under the MIT-0 License. See the LICENSE file.

THIRD-PARTY-NOTICES

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The Python U-Net Tensorflow implementation is adapted by [Kjetil Åmdal-Sævik](https://www.kaggle.com/keegil/keras-u-net-starter-lb-0-277) under an Apache 2.0 open-source license.

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