From aaeb3b17642e93a96517bc1434c4cc8860301e83 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Thu, 26 Feb 2026 09:47:32 -0500 Subject: [PATCH 1/9] release: add CITATION.cff and .zenodo.json for v0.1.0 Add citation and Zenodo metadata files following the Imageomics GitHub Repo Guide conventions. Prepares for first tagged release to capture the current state of main before merging app-separation. Co-Authored-By: Claude Opus 4.6 --- .zenodo.json | 44 ++++++++++++++++++++++++++++++++++++++++++++ CITATION.cff | 38 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 .zenodo.json create mode 100644 CITATION.cff diff --git a/.zenodo.json b/.zenodo.json new file mode 100644 index 0000000..98e7820 --- /dev/null +++ b/.zenodo.json @@ -0,0 +1,44 @@ +{ + "creators": [ + { + "name": "Zhang, Net", + "orcid": "0000-0003-2664-451X", + "affiliation": "The Ohio State University" + }, + { + "name": "Campolongo, Elizabeth G.", + "orcid": "0000-0003-0846-2413", + "affiliation": "The Ohio State University" + }, + { + "name": "Thompson, Matthew J.", + "orcid": "0000-0003-0583-8585" + }, + { + "name": "Menon, Sreejith" + }, + { + "name": "Gu, Jianyang" + }, + { + "name": "Nandi, Arnab" + } + ], + "title": "emb-explorer", + "description": "Image clustering tool using embeddings with Streamlit interface. Supports GPU-accelerated dimensionality reduction and clustering with automatic CPU fallback.", + "version": "0.1.0", + "license": "MIT", + "publication_date": "2026-02-26", + "keywords": [ + "imageomics", + "embeddings", + "clustering", + "visualization", + "streamlit", + "image-analysis" + ], + "grants": [ + {"id": "021nxhr62::2118240"}, + {"id": "021nxhr62::2330423"} + ] +} diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..73f70d3 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,38 @@ +cff-version: 1.2.0 +title: emb-explorer +abstract: >- + Image clustering tool using embeddings with Streamlit interface. + Supports GPU-accelerated dimensionality reduction and clustering + with automatic CPU fallback. +message: >- + If you use this software in your research, please cite it as below. +type: software +authors: + - family-names: Zhang + given-names: Net + orcid: "https://orcid.org/0000-0003-2664-451X" + affiliation: The Ohio State University + - family-names: Campolongo + given-names: Elizabeth G. + orcid: "https://orcid.org/0000-0003-0846-2413" + affiliation: The Ohio State University + - family-names: Thompson + given-names: Matthew J. + orcid: "https://orcid.org/0000-0003-0583-8585" + - family-names: Menon + given-names: Sreejith + - family-names: Gu + given-names: Jianyang + - family-names: Nandi + given-names: Arnab +version: 0.1.0 +date-released: "2026-02-26" +license: MIT +repository-code: https://github.com/Imageomics/emb-explorer +keywords: + - imageomics + - embeddings + - clustering + - visualization + - streamlit + - image-analysis From 62e21188e19a4a483af836cae89344b0e17b425b Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Thu, 26 Feb 2026 09:48:44 -0500 Subject: [PATCH 2/9] release: add author ORCIDs and affiliations Co-Authored-By: Claude Opus 4.6 --- .zenodo.json | 15 +++++++++++---- CITATION.cff | 7 +++++++ 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 98e7820..ad97ca1 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -12,16 +12,23 @@ }, { "name": "Thompson, Matthew J.", - "orcid": "0000-0003-0583-8585" + "orcid": "0000-0003-0583-8585", + "affiliation": "The Ohio State University" }, { - "name": "Menon, Sreejith" + "name": "Menon, Sreejith", + "orcid": "0009-0009-6277-2413", + "affiliation": "Google" }, { - "name": "Gu, Jianyang" + "name": "Gu, Jianyang", + "orcid": "0000-0002-4060-7427", + "affiliation": "The Ohio State University" }, { - "name": "Nandi, Arnab" + "name": "Nandi, Arnab", + "orcid": "0000-0002-4138-603X", + "affiliation": "The Ohio State University" } ], "title": "emb-explorer", diff --git a/CITATION.cff b/CITATION.cff index 73f70d3..8ab1ed5 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -19,12 +19,19 @@ authors: - family-names: Thompson given-names: Matthew J. orcid: "https://orcid.org/0000-0003-0583-8585" + affiliation: The Ohio State University - family-names: Menon given-names: Sreejith + orcid: "https://orcid.org/0009-0009-6277-2413" + affiliation: Google - family-names: Gu given-names: Jianyang + orcid: "https://orcid.org/0000-0002-4060-7427" + affiliation: The Ohio State University - family-names: Nandi given-names: Arnab + orcid: "https://orcid.org/0000-0002-4138-603X" + affiliation: The Ohio State University version: 0.1.0 date-released: "2026-02-26" license: MIT From 408bc6d05d2aa8255e32096141264f4638ff1b16 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Thu, 26 Feb 2026 09:56:51 -0500 Subject: [PATCH 3/9] release: align with pybioclip conventions Use object format for license in .zenodo.json and add url field to CITATION.cff, matching pybioclip's established pattern. Co-Authored-By: Claude Opus 4.6 --- .zenodo.json | 3 +-- CITATION.cff | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index ad97ca1..8485799 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -34,14 +34,13 @@ "title": "emb-explorer", "description": "Image clustering tool using embeddings with Streamlit interface. Supports GPU-accelerated dimensionality reduction and clustering with automatic CPU fallback.", "version": "0.1.0", - "license": "MIT", + "license": {"id": "MIT"}, "publication_date": "2026-02-26", "keywords": [ "imageomics", "embeddings", "clustering", "visualization", - "streamlit", "image-analysis" ], "grants": [ diff --git a/CITATION.cff b/CITATION.cff index 8ab1ed5..8071da1 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -36,10 +36,10 @@ version: 0.1.0 date-released: "2026-02-26" license: MIT repository-code: https://github.com/Imageomics/emb-explorer +url: https://github.com/Imageomics/emb-explorer keywords: - imageomics - embeddings - clustering - visualization - - streamlit - image-analysis From 4e1eed72257e28933d9b3fbe05dac1d669d334c2 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Thu, 26 Feb 2026 10:03:54 -0500 Subject: [PATCH 4/9] release: remove unrelated grant from .zenodo.json Keep only NSF HDR Imageomics Institute grant (2118240). Co-Authored-By: Claude Opus 4.6 --- .zenodo.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 8485799..bd58316 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -44,7 +44,6 @@ "image-analysis" ], "grants": [ - {"id": "021nxhr62::2118240"}, - {"id": "021nxhr62::2330423"} + {"id": "021nxhr62::2118240"} ] } From c8e11a808dd3d03320875f2b723924e9736a0cd4 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Thu, 26 Feb 2026 12:00:27 -0500 Subject: [PATCH 5/9] Format `CITATION.cff` & `.zenodo.json` - Format `CITATION.cff` & `.zenodo.json` to stay consistent to the imageomics repo guide template - Added Hilmar to the author list - Copy-and-pasted the zenodo validation file from guide --- .github/workflows/validate-zenodo.yaml | 23 +++++++++++++++++++ .zenodo.json | 16 +++++++++---- CITATION.cff | 31 ++++++++++++++++++-------- 3 files changed, 57 insertions(+), 13 deletions(-) create mode 100644 .github/workflows/validate-zenodo.yaml diff --git a/.github/workflows/validate-zenodo.yaml b/.github/workflows/validate-zenodo.yaml new file mode 100644 index 0000000..e640ec7 --- /dev/null +++ b/.github/workflows/validate-zenodo.yaml @@ -0,0 +1,23 @@ +name: Check zenodo metadata + +on: + push: + paths: + - '.zenodo.json' + - '.github/workflows/validate-zenodo.yaml' + +jobs: + check-zenodo-metadata: + + runs-on: ubuntu-latest + + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 + with: + node-version: '22' + - name: Install dependencies + run: npm install zenodraft@0.14.1 + - name: Check .zenodo.json file + run: | + npx zenodraft metadata validate .zenodo.json \ No newline at end of file diff --git a/.zenodo.json b/.zenodo.json index bd58316..dfbd135 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -15,6 +15,11 @@ "orcid": "0000-0003-0583-8585", "affiliation": "The Ohio State University" }, + { + "name": "Hilmar, Lapp", + "orcid": "0000-0001-9107-0714", + "affiliation": "Neuromatch, Inc." + }, { "name": "Menon, Sreejith", "orcid": "0009-0009-6277-2413", @@ -31,11 +36,7 @@ "affiliation": "The Ohio State University" } ], - "title": "emb-explorer", "description": "Image clustering tool using embeddings with Streamlit interface. Supports GPU-accelerated dimensionality reduction and clustering with automatic CPU fallback.", - "version": "0.1.0", - "license": {"id": "MIT"}, - "publication_date": "2026-02-26", "keywords": [ "imageomics", "embeddings", @@ -43,6 +44,13 @@ "visualization", "image-analysis" ], + "title": "emb-explorer", + + "version": "0.1.0", + + "license": {"id": "MIT"}, + "publication_date": "2026-02-26", + "grants": [ {"id": "021nxhr62::2118240"} ] diff --git a/CITATION.cff b/CITATION.cff index 8071da1..923f536 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,12 +1,7 @@ -cff-version: 1.2.0 -title: emb-explorer abstract: >- Image clustering tool using embeddings with Streamlit interface. Supports GPU-accelerated dimensionality reduction and clustering with automatic CPU fallback. -message: >- - If you use this software in your research, please cite it as below. -type: software authors: - family-names: Zhang given-names: Net @@ -20,6 +15,11 @@ authors: given-names: Matthew J. orcid: "https://orcid.org/0000-0003-0583-8585" affiliation: The Ohio State University + - family-names: Hilmar + given-names: Lapp + affiliation: Neuromatch, Inc. + orcid: "https://orcid.org/0000-0001-9107-0714" + affiliation: The Ohio State University - family-names: Menon given-names: Sreejith orcid: "https://orcid.org/0009-0009-6277-2413" @@ -32,14 +32,27 @@ authors: given-names: Arnab orcid: "https://orcid.org/0000-0002-4138-603X" affiliation: The Ohio State University -version: 0.1.0 +cff-version: 1.2.0 date-released: "2026-02-26" -license: MIT -repository-code: https://github.com/Imageomics/emb-explorer -url: https://github.com/Imageomics/emb-explorer +identifiers: + # TODO: update after release + - description: "The GitHub release URL of tag ." + type: url + value: "https://github.com/Imageomics/emb-explorer/releases/tag/" + # TODO: update after release + - description: "The GitHub URL of the commit tagged with ." + type: url + value: "https://github.com/Imageomics/emb-explorer/tree/" keywords: - imageomics - embeddings - clustering - visualization - image-analysis +license: MIT +message: "If you find this software helpful in your research, please cite both the software." +repository-code: "https://github.com/Imageomics/emb-explorer" +title: "emb-explorer" +version: 0.1.0 +doi: # TODO: update after ZENODO release +type: software \ No newline at end of file From 9f0c28a32e884bb84beec8ebcaabce75615630d2 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Fri, 27 Feb 2026 15:22:24 -0500 Subject: [PATCH 6/9] Add reference for core SDK Co-authored-by: Elizabeth Campolongo <38985481+egrace479@users.noreply.github.com> --- .zenodo.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index dfbd135..37c8f12 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -53,5 +53,11 @@ "grants": [ {"id": "021nxhr62::2118240"} + ], + + "references": [ + "Ilharco, G., Wortsman, M., Wightman, R., Gordon, C., Carlini, N., Taori, R., Dave, A., Shankar, V., Namkoong, H., Miller, J., Hajishirzi, H., Farhadi, A., & Schmidt, L. (2021). OpenCLIP [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.5143773", + "VanderPlas, J., Granger, B. E., Heer, J., Moritz, D., Wongsuphasawat, K., Satyanarayan, A., Lees, E., Timofeev, I., Welsh, B., & Sievert, S. (2018). Altair: Interactive Statistical Visualizations for Python. Journal of Open Source Software, 3(32), 1057. https://doi.org/10.21105/joss.01057", + "Streamlit (Version 1.40.0) [Computer software]. (2024). Snowflake Inc. https://github.com/streamlit/streamlit" ] } From 37e7367f4ffe81ac64faaf9d0a5a9cbde9b234af Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Mon, 2 Mar 2026 15:13:25 -0500 Subject: [PATCH 7/9] Change title to Image Embedding Explorer --- .zenodo.json | 2 +- CITATION.cff | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 37c8f12..4d0d22f 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -44,7 +44,7 @@ "visualization", "image-analysis" ], - "title": "emb-explorer", + "title": "Image Embedding Explorer", "version": "0.1.0", diff --git a/CITATION.cff b/CITATION.cff index 923f536..686cc2d 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -52,7 +52,7 @@ keywords: license: MIT message: "If you find this software helpful in your research, please cite both the software." repository-code: "https://github.com/Imageomics/emb-explorer" -title: "emb-explorer" +title: "Image Embedding Explorer" version: 0.1.0 doi: # TODO: update after ZENODO release type: software \ No newline at end of file From 9c90e8230ec7c165a2677d2981a02d63a39e4fc6 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Mon, 2 Mar 2026 15:15:12 -0500 Subject: [PATCH 8/9] Specify Pre-release Tag --- CITATION.cff | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 686cc2d..7e60c80 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -35,12 +35,11 @@ authors: cff-version: 1.2.0 date-released: "2026-02-26" identifiers: - # TODO: update after release - - description: "The GitHub release URL of tag ." + - description: "The GitHub release URL of tag v0.1.0." type: url - value: "https://github.com/Imageomics/emb-explorer/releases/tag/" + value: "https://github.com/Imageomics/emb-explorer/releases/tag/v0.1.0" # TODO: update after release - - description: "The GitHub URL of the commit tagged with ." + - description: "The GitHub URL of the commit tagged with v0.1.0." type: url value: "https://github.com/Imageomics/emb-explorer/tree/" keywords: From e7d0b2476df0ecd82b3e5fc1bf258f195c274861 Mon Sep 17 00:00:00 2001 From: Net Zhang Date: Mon, 2 Mar 2026 15:16:30 -0500 Subject: [PATCH 9/9] Update Release Date --- .zenodo.json | 2 +- CITATION.cff | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 4d0d22f..fa9dc55 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -49,7 +49,7 @@ "version": "0.1.0", "license": {"id": "MIT"}, - "publication_date": "2026-02-26", + "publication_date": "2026-03-02", "grants": [ {"id": "021nxhr62::2118240"} diff --git a/CITATION.cff b/CITATION.cff index 7e60c80..eb97f0c 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -33,7 +33,7 @@ authors: orcid: "https://orcid.org/0000-0002-4138-603X" affiliation: The Ohio State University cff-version: 1.2.0 -date-released: "2026-02-26" +date-released: "2026-03-02" identifiers: - description: "The GitHub release URL of tag v0.1.0." type: url