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Fix links by removing header symbol
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jimmymathews committed Sep 23, 2024
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Expand Up @@ -4,14 +4,14 @@ The scripts here are used to import dataset into a PostgreSQL database for the S
2. [Doing import / upload into the database](#doing-import--upload-into-the-database)
3. [Finer control of upload process](#finer-control-of-upload-process)

# 1. Curation or pre-processing
# Curation or pre-processing

Datasets are stored in subdirectories of `datasets/`. To prepare a new dataset, follow the full example [here](`datasets/moldoveanu/README.md`). The example includes files pre-generated in a format ready for import into the database, but you can also re-generate them yourself.

Extraction scripts tend to be dataset-specific, but there are some common tasks like quantification over segments in images, and formulation of standardized representations of channel or clinical metadata.


# 2. Doing import / upload into the database
# Doing import / upload into the database
Make sure that
- [`spatialprofilingtoolbox` Python package](https://pypi.org/project/spatialprofilingtoolbox/) has been installed, and
- PostgresQL is installed and running on your machine.
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- `moldoveanu` is the name of the dataset subdirectory for the complete example.


# 3. Finer control of the upload process
# Finer control of the upload process
The usage above uses several convenience wrapper functions, and assumes that you have saved dataset artifacts to `datasetes/<dataset_name>/generated_artifacts/`.

For finer control, for example when drawing source files from an S3 bucket, use the following:
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