# Contributing

We welcome contributions to the Cell Painting Gallery.

## Contributing to Documentation

If you would like to contribute to our documentation, please make a [Pull Request](https://github.com/broadinstitute/cellpainting-gallery/pulls).
We particularly welcome contributions to our list of [publications using data from the Cell Painting Gallery](publications.md) and to [workflows accessing the Cell Painting Gallery](workflows.md).

To ask a question that is not covered by our documentation, you are also welcome to create an [Issue](https://github.com/broadinstitute/cellpainting-gallery/issues) in the Cell Painting Gallery repository.
Please note that the Cell Painting Gallery is not a place to ask dataset-specific questions.
Instead, please direct such questions to the respective dataset repository linked in [Complete Datasets](complete_datasets.md) or if no dataset repository, to the authors of any associated publication.

## Contributing Data to the Gallery

Contributions can be in the form of complete datasets (can be images and metadata or images and a complete `workspace`) or additions to extant datasets (e.g. segmentations or deep-learning generated profiles).
Please contact @erinweisbart or @shntnu to initiate discussion of a data contribution.

For new datasets, please include the following details in your contact:

1) assay used (standard Cell Painting or describe the variation. If you would like to contribute data from a derivative assay it must be useable for morphological profiling in that it stains/labels multiple cellular compartments/organelles.)
2) approximate data size
3) components you wish to contribute (all are described in [data structure](data_structure.md)) (major components: `images`, `analysis`, `backend`, `load_data_csv`, `profiles`. optional components: `pipelines`, `qc`, etc.). **Note that `images`, `metadata` and `load_data_csv` are required.**
4) institutional identifier to use for data (e.g. `broad`, `anonymous`)
5) suggested top level project tag.
We will assign the cpg number but are happy to take suggestions for the tag appended to the cpg number.
The tag is typically a 1 word summary of the project (e.g. cpg0011-lipocyteprofiler, cpg0016-jump, cpg0022-cmqtl) and sometimes also includes the last name of the first author (e.g. cpg0010-caie-drugresponse, cpg0028-kelley-resistance, cpg0031-caicedo-cmvip)

For existing datasets, please  the following details include in your contact:

1) top-level project tag that your data corresponds to (e.g. `cpg0016-jump`)
2) approximate data size
3) components you wish to contribute

After approval, we will assign you a project identifier and create a new [Github Discussion](https://github.com/broadinstitute/cellpainting-gallery/discussions) using our [discussion template](https://github.com/broadinstitute/cellpainting-gallery/discussions/66) to provide next steps and track data deposition.

## Preparing for data deposition

In preparation for transferring data, please perform all of the following steps:

### Remove special characters in folder names

To the maximum extent possible, please avoid the following in your folder names (delete them if present):

- Whitespaces
- Special characters other than `_` and `-`

### Prepare project-specific naming

Reference [data structure](data_structure.md) for comprehensive information on folder structure and naming.
Your data must strictly comply with the data structure we have laid out.
Additionally it must include all, unblinded metadata - this means that the minimum dataset contribution is `images`, `metadata`, and `load_data_csv`.

### Validate your data

Currently, validation is performed by Erin/Shantanu after data is uploaded to staging. In the future we plan on having contributors first validate their data before any upload.

### Create a pull-request

Any data contributions to Cell Painting Gallery must be accompanied by a pull request to the [Cell Painting Gallery repository](https://github.com/broadinstitute/cellpainting-gallery/) with updates to the README to add your dataset to [Available datasets](https://github.com/broadinstitute/cellpainting-gallery/blob/main/README.md).
If your dataset is associated with a publication, please also edit [Publications](https://github.com/broadinstitute/cellpainting-gallery/blob/main/documentation/publications.md).