From 5d9c25e46cabefab687bbe3bbd179a5fbc582682 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Wed, 29 Nov 2023 16:46:51 -0700 Subject: [PATCH 1/9] updated readme with preprint --- README.md | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index c257682b..3788b7ff 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 +203,10 @@ pycytominer.cyto_utils.write_gct( output_file=output_file ) ``` + +## Citing pycytominer + +If you have used the `pycytominer` in your work, please consider citing our preprint: + +>Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. (2023): [Reproducible image-based profiling with Pycytominer](https://arxiv.org/abs/2311.13417) +> DOI: From a45a99eaef6eb265c24a9e79635619e8c828fa82 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Wed, 29 Nov 2023 17:14:41 -0700 Subject: [PATCH 2/9] applied pre-commit --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3788b7ff..57e7cba2 100644 --- a/README.md +++ b/README.md @@ -208,5 +208,5 @@ pycytominer.cyto_utils.write_gct( If you have used the `pycytominer` in your work, please consider citing our preprint: ->Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. (2023): [Reproducible image-based profiling with Pycytominer](https://arxiv.org/abs/2311.13417) +> Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. (2023): [Reproducible image-based profiling with Pycytominer](https://arxiv.org/abs/2311.13417) > DOI: From a36cc3b7aa3ba651bbea6d6c78d7947a7590b4aa Mon Sep 17 00:00:00 2001 From: axiomcura Date: Thu, 30 Nov 2023 09:58:41 -0700 Subject: [PATCH 3/9] update author list CFF --- CITATION.cff | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index 72281560..835b96ef 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 From 5c7e8ef2cb8be4a19bff7d688a6c6c782b166837 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Thu, 30 Nov 2023 10:00:53 -0700 Subject: [PATCH 4/9] updated title; added doi in cff file --- CITATION.cff | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 835b96ef..fa0b28dd 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -83,8 +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 From c15c7a52abbeaeefe58dc1334093807c79fa5d37 Mon Sep 17 00:00:00 2001 From: Erik Serrano <31600622+axiomcura@users.noreply.github.com> Date: Sat, 2 Dec 2023 17:47:31 -0700 Subject: [PATCH 5/9] Update README.md Co-authored-by: Gregory Way --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 57e7cba2..8fb5b194 100644 --- a/README.md +++ b/README.md @@ -206,7 +206,7 @@ pycytominer.cyto_utils.write_gct( ## Citing pycytominer -If you have used the `pycytominer` in your work, please consider citing our preprint: +If you have used `pycytominer` in your work, please consider citing our preprint: > Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. (2023): [Reproducible image-based profiling with Pycytominer](https://arxiv.org/abs/2311.13417) > DOI: From 7cf593db4b5ed36547f45156ad342ffc66d39c89 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Mon, 4 Dec 2023 09:50:35 -0700 Subject: [PATCH 6/9] update --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 8fb5b194..897f2810 100644 --- a/README.md +++ b/README.md @@ -206,7 +206,8 @@ pycytominer.cyto_utils.write_gct( ## Citing pycytominer -If you have used `pycytominer` in your work, please consider citing our preprint: +If you have used `pycytominer` in your project, please cite us as: + +> Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. ["Reproducible image-based profiling with Pycytominer"](https://arxiv.org/abs/2311.13417) _ArXiv: Quantitative Biology_, 2023 -> Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. (2023): [Reproducible image-based profiling with Pycytominer](https://arxiv.org/abs/2311.13417) > DOI: From 4db798bd393d71715dc3c21af9a81ee1d82a9bc0 Mon Sep 17 00:00:00 2001 From: axiomcura Date: Mon, 4 Dec 2023 10:08:24 -0700 Subject: [PATCH 7/9] updated citing section --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 897f2810..95f84367 100644 --- a/README.md +++ b/README.md @@ -206,8 +206,10 @@ pycytominer.cyto_utils.write_gct( ## Citing pycytominer -If you have used `pycytominer` in your project, please cite us as: +If you have used `pycytominer` in your project, please use citation below: You can also find the citation in the 'cite this repository' link at the top right under `about` section. -> Erik Serrano, Srinivas Niranj Chandrasekaran, Dave Bunten, Kenneth I. Brewer, Jenna Tomkinson, Roshan Kern, Michael Bornholdt, Stephen Fleming, Ruifan Pei, John Arevalo, Hillary Tsang, Vincent Rubinetti, Callum Tromans-Coia, Tim Becker, Erin Weisbart, Charlotte Bunne, Alexandr A. Kalinin, Rebecca Senft, Stephen J. Taylor, Nasim Jamali, Adeniyi Adeboye, Hamdah Shafqat Abbasi, Allen Goodman, Juan C. Caicedo, Anne E. Carpenter, Beth A. Cimini, Shantanu Singh, Gregory P. Way. ["Reproducible image-based profiling with Pycytominer"](https://arxiv.org/abs/2311.13417) _ArXiv: Quantitative Biology_, 2023 +APA: -> DOI: +```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 (Version 1.0.1) [Computer software]. https://doi.org/10.48550/arXiv.2311.13417 +``` From d3981b6d8f3de9405dafdd7684b16b7e7d2a6328 Mon Sep 17 00:00:00 2001 From: Erik Serrano <31600622+axiomcura@users.noreply.github.com> Date: Mon, 4 Dec 2023 10:28:55 -0700 Subject: [PATCH 8/9] Update README.md Co-authored-by: Ken Brewer --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 95f84367..99952578 100644 --- a/README.md +++ b/README.md @@ -206,7 +206,8 @@ pycytominer.cyto_utils.write_gct( ## Citing pycytominer -If you have used `pycytominer` in your project, please use citation below: You can also find the citation in the 'cite this repository' link at the top right under `about` section. +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: From b51dbe35ea3aa61c2622b58575b346e6812006ab Mon Sep 17 00:00:00 2001 From: Erik Serrano <31600622+axiomcura@users.noreply.github.com> Date: Mon, 4 Dec 2023 10:29:28 -0700 Subject: [PATCH 9/9] Update README.md Co-authored-by: Ken Brewer --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 99952578..0f646c47 100644 --- a/README.md +++ b/README.md @@ -212,5 +212,5 @@ You can also find the citation in the 'cite this repository' link at the top rig 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 (Version 1.0.1) [Computer software]. https://doi.org/10.48550/arXiv.2311.13417 +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 ```