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ctr26 authored Sep 25, 2023
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# Installation

pip install git+https://github.com/ctr26/bio_vae
pip install git+https://github.com/ctr26/bioimage_embed



# Mask-VAE
# Shape-Embed

This project attempts to using modern auto-encoding CNNs to access the latent shape space of a given dataset.
We demonstrate this on microscopy images of nuclei and C. Elegans (worms).
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If you don't have a Kaggle account you must create one and then follow the next steps:
1. Install the Kaggle API package so you can download the data from the Makefile you have all the information in their [Github repository](https://github.com/Kaggle/kaggle-api).
2. To use the Kaggle API you need also to create an API token. You can found how to do it in their [documentation](https://github.com/Kaggle/kaggle-api#api-credentials)
3. After that you will need to add your user and key in a file called `kaggle.json` in this location in your home directory `chmod 600 ~/.kaggle/kaggle.json`
4. Don't forget to accept the conditions for the "2018 Data Science Bowl" on the Kaggle website. Otherwise you would not be able to pull this data from the command line.
2. To use the Kaggle API you need also to create an API token.
You can found how to do it in their [documentation](https://github.com/Kaggle/kaggle-api#api-credentials)
4. After that you will need to add your user and key in a file called `kaggle.json` in this location in your home directory `chmod 600 ~/.kaggle/kaggle.json`
5. Don't forget to accept the conditions for the "2018 Data Science Bowl" on the Kaggle website.
Otherwise you would not be able to pull this data from the command line.

### Install

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