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1 | | -## My Project |
| 1 | +# Biological Cell Segmentation using Amazon SageMaker |
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3 | | -TODO: Fill this README out! |
| 3 | +> 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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5 | | -Be sure to: |
| 5 | +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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7 | | -* Change the title in this README |
8 | | -* Edit your repository description on GitHub |
| 7 | +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: |
| 8 | + |
| 9 | +* Downloading the dataset from the Broad Bioimage Benchmark Collection (BBBC005) which will be used for training purposes to build our model. |
| 10 | +* Demonstrate the process to use a SageMaker Notebook to train a model form scratch, specifically for cell-segmentation. |
| 11 | +* Setting up an SageMaker Inference endpoint to host our model. |
| 12 | +* 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. |
| 13 | + |
| 14 | +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. |
| 15 | + |
| 16 | +## Training architecture |
| 17 | + |
| 18 | +The architecture for training the model consists of the following: |
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| 20 | + |
| 21 | + |
| 22 | +## Inference architecture |
| 23 | + |
| 24 | +The architecture for running inference consists of the following: |
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| 26 | + |
| 27 | + |
| 28 | +## Next steps |
| 29 | + |
| 30 | +Please see the AWS Workshop for a complete tutorial on using this repository. |
| 31 | + |
| 32 | +https://catalog.us-east-1.prod.workshops.aws/workshops/7fb985db-2c2c-4f72-8aa6-7a1c8202b61a |
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10 | 34 | ## Security |
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12 | 36 | See [CONTRIBUTING](CONTRIBUTING.md#security-issue-notifications) for more information. |
13 | 37 |
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14 | 38 | ## License |
15 | 39 |
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16 | | -This library is licensed under the MIT-0 License. See the LICENSE file. |
17 | | - |
| 40 | +This library is licensed under the MIT-0 License. See the LICENSE file. |
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