diff --git a/CITATION.cff b/CITATION.cff index 72281560..fa0b28dd 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -26,33 +26,51 @@ authors: orcid: https://orcid.org/0000-0002-1885-4405 - family-names: Pei given-names: Ruifan + orcid: https://orcid.org/0009-0003-4964-2821 - family-names: Arevalo given-names: John orcid: https://orcid.org/0000-0002-1138-5036 - family-names: Tsang given-names: Hillary + orcid: https://orcid.org/0000-0001-6461-3402 - family-names: Rubinetti given-names: Vincent + orcid: https://orcid.org/0000-0002-4655-3773 + - family-names: Tromans-Coia + given-names: Callum + orcid: https://orcid.org/0000-0002-5518-8915 + - family-names: Becker + given-names: Tim + orcid: https://orcid.org/0000-0001-9615-0799 - family-names: Weisbart given-names: Erin orcid: https://orcid.org/0000-0002-6437-2458 - family-names: Bunne given-names: Charlotte + orcid: https://orcid.org/0000-0003-1431-103X - family-names: Kalinin given-names: Alexandr A. + orcid: https://orcid.org/0000-0003-4563-3226 - family-names: Senft given-names: Rebecca + orcid: https://orcid.org/0000-0003-0081-4170 - family-names: Taylor given-names: Stephen J. orcid: https://orcid.org/0000-0002-7279-7798 - family-names: Jamali given-names: Nasim + orcid: https://orcid.org/0000-0003-1851-6585 - family-names: Adeboye given-names: Adeniyi + - family-names: Abbasi + given-names: Hamdah Shafqat + orcid: https://orcid.org/0000-0003-0237-0323 - family-names: Goodman given-names: Allen + orcid: https://orcid.org/0000-0002-6434-2320 - family-names: Caicedo given-names: Juan + orcid: https://orcid.org/0000-0002-1277-4631 - family-names: Carpenter given-names: Anne E. orcid: https://orcid.org/0000-0003-1555-8261 @@ -65,8 +83,9 @@ authors: - family-names: Way given-names: Gregory P. orcid: https://orcid.org/0000-0002-0503-9348 -title: "Reproducible processing of image-based profiling representations with Pycytominer" +title: "Reproducible image-based profiling with Pycytominer" # This version is updated using `cz bump` command version: "1.0.1" license: BSD 3-Clause License repository-code: "https://github.com/cytomining/pycytominer" +doi: 10.48550/arXiv.2311.13417 diff --git a/README.md b/README.md index c257682b..0f646c47 100644 --- a/README.md +++ b/README.md @@ -6,6 +6,7 @@ [![Coverage Status](https://codecov.io/gh/cytomining/pycytominer/branch/main/graph/badge.svg)](https://codecov.io/github/cytomining/pycytominer?branch=main) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black) [![RTD](https://readthedocs.org/projects/pycytominer/badge/?version=latest&style=flat)](https://pycytominer.readthedocs.io/) +[![DOI](https://img.shields.io/badge/DOI-10.48550/arXiv.2311.13417-blue)](https://doi.org/10.48550/arXiv.2311.13417) Pycytominer is a suite of common functions used to process high dimensional readouts from high-throughput cell experiments. The tool is most often used for processing data through the following pipeline: @@ -110,9 +111,17 @@ And, more specifically than that, image-based profiling readouts from [CellProfi Therefore, we have included some custom tools in `pycytominer/cyto_utils` that provides other functionality: -- [CellProfiler CSV collation](#CellProfiler-CSV-collation) -- [Cell locations lookup table generation](#Creating-a-cell-locations-lookup-table) -- [Generating gct files for Morpheus visualization](#Generating-a-GCT-file-for-morpheus) +- [Data processing for image-based profiling](#data-processing-for-image-based-profiling) + - [Installation](#installation) + - [Frameworks](#frameworks) + - [API](#api) + - [Usage](#usage) + - [Pipeline orchestration](#pipeline-orchestration) + - [Other functionality](#other-functionality) + - [CellProfiler CSV collation](#cellprofiler-csv-collation) + - [Creating a cell locations lookup table](#creating-a-cell-locations-lookup-table) + - [Generating a GCT file for morpheus](#generating-a-gct-file-for-morpheus) + - [Citing pycytominer](#citing-pycytominer) Note, [`pycytominer.cyto_utils.cells.SingleCells()`](pycytominer/cyto_utils/cells.py) contains code to interact with single-cell SQLite files, which are output from CellProfiler. Processing capabilities for SQLite files depends on SQLite file size and your available computational resources (for ex. memory and cores). @@ -194,3 +203,14 @@ pycytominer.cyto_utils.write_gct( output_file=output_file ) ``` + +## Citing pycytominer + +If you have used `pycytominer` in your project, please use the citation below. +You can also find the citation in the 'cite this repository' link at the top right under `about` section. + +APA: + +```text +Serrano, E., Chandrasekaran, N., Bunten, D., Brewer, K., Tomkinson, J., Kern, R., Bornholdt, M., Fleming, S., Pei, R., Arevalo, J., Tsang, H., Rubinetti, V., Tromans-Coia, C., Becker, T., Weisbart, E., Bunne, C., Kalinin, A. A., Senft, R., Taylor, S. J., Jamali, N., Adeboye, A., Abbasi, H. S., Goodman, A., Caicedo, J., Carpenter, A. E., Cimini, B. A., Singh, S., & Way, G. P. Reproducible image-based profiling with Pycytominer. https://doi.org/10.48550/arXiv.2311.13417 +```