From 95562f57998bdd8e6cfe827095064f3064f54a87 Mon Sep 17 00:00:00 2001 From: Draga Doncila Date: Thu, 21 Aug 2025 16:37:16 +1000 Subject: [PATCH 1/6] Add basic citation file --- CITATION.cff | 86 ++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..29c2d813 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,86 @@ +cff-version: 1.2.0 +message: If you use this software, please cite it using these metadata. +title: 'GEFF: Graph Exchange File Format' +authors: + - given-names: Morgan + family-names: Schwartz + affiliation: Janelia Research Campus + orcid: https://orcid.org/0000-0001-8131-9125 + alias: msschwartz21 + - given-names: Caroline + family-names: Malin-Mayor + affiliation: Janelia Research Campus + orcid: https://orcid.org/0000-0002-9627-6030 + alias: cmalinmayor + - given-names: Talley + family-names: Lambert + affiliation: Harvard Medical School + orcid: https://orcid.org/0000-0002-2409-0181 + alias: tlambert03 + - given-names: Teun + family-names: Huijben + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: https://orcid.org/0000-0002-8984-2882 + alias: TeunHuijben + - given-names: Jan + family-names: Funke + affiliation: Janelia Research Campus + orcid: https://orcid.org/0000-0003-4388-7783 + alias: funkey + - given-names: Laura + family-names: Xénard + affiliation: Institut Pasteur + orcid: https://orcid.org/0000-0002-8168-0970 + alias: lxenard + - given-names: Mark + family-names: Kittisopikul + affiliation: Janelia Research Campus + orcid: https://orcid.org/0000-0002-9558-6248 + alias: mkitti + - given-names: Draga + family-names: Doncila Pop + affiliation: Monash University + orcid: https://orcid.org/0000-0001-9116-5553 + alias: DragaDoncila + - given-names: Yohsuke + family-names: Fukai + affiliation: RIKEN Center for Biosystems Dynamics Research + orcid: https://orcid.org/0000-0002-8860-7178 + alias: yfukai + - given-names: Jordão + family-names: Bragantini + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: https://orcid.org/0000-0001-7652-2735 + alias: JoOkuma + - given-names: Melisande + family-names: Croft + affiliation: Human Technopole + orcid: https://orcid.org/0009-0004-8184-683X + alias: melisande-c + - given-names: Anniek + family-names: Stokkermans + affiliation: Hubrecht Institute + orcid: https://orcid.org/0000-0002-9013-9983 + alias: AnniekStok + - given-names: Georgeos + family-names: Hardo + affiliation: UAE University + orcid: https://orcid.org/0000-0003-0037-1293 + alias: georgeoshardo + - given-names: Benjamin + family-names: Gallusser + affiliation: Chan Zuckerbeg Initiative + orcid: https://orcid.org/0000-0002-7906-4714 + alias: bentaculum + - given-names: Kasia + family-names: Kedziora + affiliation: University of Pittsburgh + orcid: https://orcid.org/0000-0001-6524-7731 + alias: fjorka + - given-names: Jean-Yves + family-names: Tinevez + affiliation: Institut Pasteur + orcid: https://orcid.org/0000-0002-0998-4718 + alias: tinevez +license: MIT +repository-code: https://github.com/live-image-tracking-tools/geff \ No newline at end of file From efb66d73f6ccf9255d916230c475c4b19f58383d Mon Sep 17 00:00:00 2001 From: Morgan Schwartz Date: Thu, 21 Aug 2025 16:56:54 -0400 Subject: [PATCH 2/6] Update yfukai affiliation Co-authored-by: Yohsuke T. Fukai --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index 29c2d813..acdecfef 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -44,7 +44,7 @@ authors: alias: DragaDoncila - given-names: Yohsuke family-names: Fukai - affiliation: RIKEN Center for Biosystems Dynamics Research + affiliation: RIKEN Pioneering Research Institute orcid: https://orcid.org/0000-0002-8860-7178 alias: yfukai - given-names: Jordão From 179515fd7e7168dd56fc809d9a4bd7ba08d02ace Mon Sep 17 00:00:00 2001 From: Draga Doncila Date: Fri, 22 Aug 2025 16:47:32 +1000 Subject: [PATCH 3/6] Add geff-java contributors --- CITATION.cff | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/CITATION.cff b/CITATION.cff index acdecfef..f30020d4 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -82,5 +82,15 @@ authors: affiliation: Institut Pasteur orcid: https://orcid.org/0000-0002-0998-4718 alias: tinevez + - given-names: Ko + family-names: Sugawara + affiliation: RIKEN Center for Biosystems Dynamics Research + orcid: https://orcid.org/0000-0002-1392-9340 + alias: ksugar + - given-names: Tobias + family-names: Pietzsch + affiliation: + orcid: + alias: tpietzsch license: MIT repository-code: https://github.com/live-image-tracking-tools/geff \ No newline at end of file From 9dd8638c9cf54a38fb200b6814d20b6b99f1b5a1 Mon Sep 17 00:00:00 2001 From: "Ilan F. S. Theodoro" Date: Fri, 22 Aug 2025 08:19:18 -0700 Subject: [PATCH 4/6] Add Ilan Theodoro's citation information --- CITATION.cff | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index f30020d4..cfae9c38 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -92,5 +92,10 @@ authors: affiliation: orcid: alias: tpietzsch + - given-names: Ilan + family-names: Theodoro + affiliation: Chan Zuckerberg Biohub San Francisco + orcid: https://orcid.org/0000-0003-4019-3380 + alias: ilan-theodoro license: MIT -repository-code: https://github.com/live-image-tracking-tools/geff \ No newline at end of file +repository-code: https://github.com/live-image-tracking-tools/geff From 2ad123b75757b8e7e0944cf1bc52dceba4433385 Mon Sep 17 00:00:00 2001 From: Caroline Malin-Mayor Date: Mon, 25 Aug 2025 16:36:55 -0400 Subject: [PATCH 5/6] Add HHMI to Janelia lines Co-authored-by: Mark Kittisopikul --- CITATION.cff | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index cfae9c38..45d3d12b 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -4,12 +4,12 @@ title: 'GEFF: Graph Exchange File Format' authors: - given-names: Morgan family-names: Schwartz - affiliation: Janelia Research Campus + affiliation: Janelia Research Campus, Howard Hughes Medical Institute orcid: https://orcid.org/0000-0001-8131-9125 alias: msschwartz21 - given-names: Caroline family-names: Malin-Mayor - affiliation: Janelia Research Campus + affiliation: Janelia Research Campus, Howard Hughes Medical Institute orcid: https://orcid.org/0000-0002-9627-6030 alias: cmalinmayor - given-names: Talley @@ -24,7 +24,7 @@ authors: alias: TeunHuijben - given-names: Jan family-names: Funke - affiliation: Janelia Research Campus + affiliation: Janelia Research Campus, Howard Hughes Medical Institute orcid: https://orcid.org/0000-0003-4388-7783 alias: funkey - given-names: Laura @@ -34,7 +34,7 @@ authors: alias: lxenard - given-names: Mark family-names: Kittisopikul - affiliation: Janelia Research Campus + affiliation: Janelia Research Campus, Howard Hughes Medical Institute orcid: https://orcid.org/0000-0002-9558-6248 alias: mkitti - given-names: Draga From 51787e2cfb02b7929e825abcbe70169bfb2c0e32 Mon Sep 17 00:00:00 2001 From: tpietzsch Date: Tue, 26 Aug 2025 09:11:59 +0200 Subject: [PATCH 6/6] Update tpietzsch information --- CITATION.cff | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 45d3d12b..5cdcff3a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -89,8 +89,8 @@ authors: alias: ksugar - given-names: Tobias family-names: Pietzsch - affiliation: - orcid: + affiliation: Independent Consultant + orcid: https://orcid.org/0000-0002-9477-3957 alias: tpietzsch - given-names: Ilan family-names: Theodoro