diff --git a/.gitignore b/.gitignore index 68bc17f..063a8e2 100644 --- a/.gitignore +++ b/.gitignore @@ -158,3 +158,7 @@ cython_debug/ # and can be added to the global gitignore or merged into this file. For a more nuclear # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ + +# Hugo build output +public/ +resources/_gen/ diff --git a/assets/css/custom.css b/assets/css/custom.css index 1cbe940..a910e52 100644 --- a/assets/css/custom.css +++ b/assets/css/custom.css @@ -1,3 +1,19 @@ +/* Page entrance animation โ€” single pages use
, list/section pages use
+
*/ +#main-content > article { + animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.1s both; +} +#main-content > header { + animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.1s both; +} +#main-content > section { + animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.25s both; +} + +/* Global font size reduction */ +html { + font-size: 90%; +} + /* Logo dark/light switching. Congo toggles a .dark class on via JS โ€” the native prefers-color-scheme media query inside tags does not respond @@ -63,11 +79,14 @@ html.dark .v2-pipeline-step-green { from { opacity: 0; transform: translateY(28px); } to { opacity: 1; transform: translateY(0); } } -.hero-fade-1 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.15s both; } -.hero-fade-2 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.30s both; } -.hero-fade-3 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.45s both; } -.hero-fade-4 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.60s both; } -.hero-fade-5 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.75s both; } +.hero-fade-1 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.10s both; } +.hero-fade-2 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.22s both; } +.hero-fade-3 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.34s both; } +.hero-fade-4 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.46s both; } +.hero-fade-5 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.58s both; } +.hero-fade-6 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.70s both; } +.hero-fade-7 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.82s both; } +.hero-fade-8 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.94s both; } /* List view logos */ .list-logo-light { display: block; } diff --git a/config/_default/params.toml b/config/_default/params.toml index a2debb7..2ea2781 100644 --- a/config/_default/params.toml +++ b/config/_default/params.toml @@ -1,7 +1,7 @@ colorScheme = "ocean" defaultAppearance = "light" autoSwitchAppearance = true -enableSearch = true +enableSearch = false enableCodeCopy = false [homepage] diff --git a/content/_index.md b/content/_index.md index f633a05..0c5274b 100644 --- a/content/_index.md +++ b/content/_index.md @@ -2,90 +2,3 @@ title: "Cytomining" description: "Open-source tools for single-cell image-based profiling" --- - -
- - -
- Cytomining -

Cytomining

-
- - -
-

- Open-source tools for every stage of the
single-cell image-based profiling workflow. -

-
- - -
-
- -
- ๐Ÿ”ฌ Raw Images -
- - โ†’ - - - iceberg-bioimage - - - โ†’ - - - CytoTable - - - โ†’ - - - coSMicQC - - - โ†’ - - - pycytominer - - - โ†’ - - - copairs - - - / - - - buscar - - -
-

ingest  ยท  quality control  ยท  process  ยท  evaluate

-
- - -
- - Explore tools โ†’ - - - Profiling handbook - -
- - -
- Profiling recipe - image.sc forum - Contributors - CytoData community -
- -
diff --git a/layouts/_partials/article-link.html b/layouts/_partials/article-link.html index 3c25ca4..09750a7 100644 --- a/layouts/_partials/article-link.html +++ b/layouts/_partials/article-link.html @@ -31,11 +31,11 @@ {{- end }}
- {{/* Small icon above title */}} - {{ with .Params.logoUrl }} - {{ $.Title }} icon - {{ end }}

+ {{/* Inline icon before title */}} + {{ with .Params.logoUrl }} + {{ $.Title }} icon + {{ end }} {{ with .Params.externalUrl }}
{{/* Header */}} -

Experimental Tools

-

+

Experimental Tools

+

Next-generation tools under active development in the WayScience organization, designed to become the foundation of Cytomining v2.

{{/* V2 pitch */}} -
+

What does Cytomining v2 solve?

The current Cytomining stack was designed around 2D single-cell data from CellProfiler. @@ -18,80 +18,124 @@

Experimental Tools

The tools below are purpose-built to close each of these gaps โ€” together forming a fully traceable, format-agnostic, 3D-capable profiling pipeline.

- {{/* V2 pipeline */}} -

Cytomining v2 pipeline

-
-
-
-
๐Ÿ”ฌ Raw Images
-
- - โ†’ - -
- iceberg-bioimage - catalog -
- - โ†’ - -
- OME-arrow - store -
- - โ†’ - -
-
๐Ÿ“Š Feature Extraction
-
- - โ†’ - -
- zedprofiler 3D - 3D extract -
- - โ†’ - -
- CytoTable - harmonize -
- - โ†’ - -
- coSMicQC - QC -
+ {{/* Tool list */}} +
+

Tools

+ {{ range .Pages }} + {{ partial "article-link.html" . }} + {{ end }} +
- โ†’ + {{/* V2 pipelines */}} +

Cytomining v2 pipelines

+ + {{/* Pipeline 1: standard (2D) */}} +
+

Standard (2D)

+
+
+ +
+
๐Ÿ”ฌ Raw Images
+
+ โ†’ +
+ iceberg-bioimage + catalog +
+ โ†’ +
+ OME-arrow + store +
+ โ†’ +
+
๐Ÿ“Š Feature Extraction
+ extract +
+ โ†’ +
+ CytoTable + harmonize +
+ โ†’ +
+ coSMicQC + QC +
+ โ†’ +
+ pycytominer + process +
+ โ†’ +
+ buscar + hit call +
-
- pycytominer - process
+
+
- โ†’ + {{/* Pipeline 2: 3D organoid */}} +
+

3D Organoid

+
+
+ +
+
๐Ÿ”ฌ Raw Images
+
+ โ†’ +
+ iceberg-bioimage + catalog +
+ โ†’ +
+ OME-arrow + store +
+ โ†’ +
+ zedprofiler 3D + 3D extract +
+ โ†’ +
+ CytoTable + harmonize +
+ โ†’ +
+ coSMicQC + QC +
+ โ†’ +
+ pycytominer + process +
+ โ†’ +
+ buscar + hit call +
-
- buscar - hit call
-
-

+ +

Yellow = new 3D-capable step. Purple = new data infrastructure. Blue = existing Cytomining tools.

{{/* Per-tool problem statements */}} -

What each tool solves

+

What each tool solves

-
+
๐Ÿ—„๏ธ @@ -127,11 +171,6 @@

What each

- {{/* Tool list */}} -

Tools

- {{ range .Pages }} - {{ partial "article-link.html" . }} - {{ end }}
{{ end }} diff --git a/layouts/index.html b/layouts/index.html index e6a0d4d..ae64fca 100644 --- a/layouts/index.html +++ b/layouts/index.html @@ -55,7 +55,6 @@

- Profiling recipe image.sc forum Contributors CytoData community diff --git a/public/404.html b/public/404.html deleted file mode 100644 index 7ff6c8f..0000000 --- a/public/404.html +++ /dev/null @@ -1,400 +0,0 @@ - - - - - - - - - - - - - 404 Page not found · Cytomining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
- - -
-
- -

Page Not Found ๐Ÿ˜•

-

- Error 404 -

-
-

It seems that the page you've requested does not exist.

-
- -
- - -
- - -
-
- - -

- © - 2026 - Cytomining -

- - - -
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- -
- -
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- - diff --git a/public/about/index.html b/public/about/index.html deleted file mode 100644 index 2e0c2e0..0000000 --- a/public/about/index.html +++ /dev/null @@ -1,414 +0,0 @@ - - - - - - - - - - - - - About · Cytomining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- -
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- - -
- -

About

-
-
- -
-

Cytomining is an open-source software ecosystem that maintains essential tools, workflows, and best practices for single-cell image-based profiling and microscopy data analysis research. -We are proud members of the CytoData scientific community.

- -
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- There's no articles to list here yet. -

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- © - 2026 - Cytomining -

- - - -
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- - diff --git a/public/about/index.xml b/public/about/index.xml deleted file mode 100644 index 1c4492f..0000000 --- a/public/about/index.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - About on Cytomining - http://localhost:1314/about/ - Recent content in About on Cytomining - Hugo - en - - - diff --git a/public/android-chrome-192x192.png b/public/android-chrome-192x192.png deleted file mode 100644 index baadce5..0000000 Binary files a/public/android-chrome-192x192.png and /dev/null differ diff --git a/public/android-chrome-512x512.png b/public/android-chrome-512x512.png deleted file mode 100644 index b73f257..0000000 Binary files a/public/android-chrome-512x512.png and /dev/null differ diff --git a/public/apple-touch-icon.png b/public/apple-touch-icon.png deleted file mode 100644 index e6e4e8c..0000000 Binary files a/public/apple-touch-icon.png and /dev/null differ diff --git a/public/categories/index.html b/public/categories/index.html deleted file mode 100644 index 446dd0a..0000000 --- a/public/categories/index.html +++ /dev/null @@ -1,402 +0,0 @@ - - - - - - - - - - - - - Categories · Cytomining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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Categories

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- © - 2026 - Cytomining -

- - - -
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- - diff --git a/public/categories/index.xml b/public/categories/index.xml deleted file mode 100644 index 861ad8b..0000000 --- a/public/categories/index.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - Categories on Cytomining - http://localhost:1314/categories/ - Recent content in Categories on Cytomining - Hugo - en - - - diff --git a/public/contact/index.html b/public/contact/index.html deleted file mode 100644 index c9b0113..0000000 --- a/public/contact/index.html +++ /dev/null @@ -1,417 +0,0 @@ - - - - - - - - - - - - - Contact · Cytomining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - diff --git a/public/contact/index.xml b/public/contact/index.xml deleted file mode 100644 index 2c86716..0000000 --- a/public/contact/index.xml +++ /dev/null @@ -1,11 +0,0 @@ - - - - Contact on Cytomining - http://localhost:1314/contact/ - Recent content in Contact on Cytomining - Hugo - en - - - diff --git a/public/css/main.bundle.min.035e4b76e168599b67aeb90a6a4aa9f874c79ca95b5d25f37b0900f38084a11d.css b/public/css/main.bundle.min.035e4b76e168599b67aeb90a6a4aa9f874c79ca95b5d25f37b0900f38084a11d.css deleted file mode 100644 index b4ecc26..0000000 --- a/public/css/main.bundle.min.035e4b76e168599b67aeb90a6a4aa9f874c79ca95b5d25f37b0900f38084a11d.css +++ /dev/null @@ -1 +0,0 @@ -:root{--color-neutral:255, 255, 255;--color-neutral-50:248, 250, 252;--color-neutral-100:241, 245, 249;--color-neutral-200:226, 232, 240;--color-neutral-300:203, 213, 225;--color-neutral-400:148, 163, 184;--color-neutral-500:100, 116, 139;--color-neutral-600:71, 85, 105;--color-neutral-700:51, 65, 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buscar is a Python package for reproducible hit calling in high-content screening. -Rather than averaging cells into population-level summaries, it operates on individual cell distributions to preserve biological heterogeneity and identify perturbations with on-target morphological signatures.

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iceberg-bioimage is a Python package that catalogs bioimaging data using Apache Iceberg. -It scans image stores across formats, publishes structured metadata tables, and exports layouts compatible with the Cytomining profiling ecosystem โ€” bridging raw image archives and downstream analysis pipelines.

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Experimental Tools

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- Next-generation tools under active development in the WayScience organization, - designed to become the foundation of Cytomining v2. -

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What does Cytomining v2 solve?

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- The current Cytomining stack was designed around 2D single-cell data from CellProfiler. - As the field moves toward 3D organoid imaging, larger-scale archives, and deep learning feature extraction, - several gaps have emerged: no standardized image catalog, images and features stored separately, no 3D support, and hit calling that collapses single-cell heterogeneity. - The tools below are purpose-built to close each of these gaps โ€” together forming a fully traceable, format-agnostic, 3D-capable profiling pipeline. -

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What each tool solves

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iceberg-bioimage

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Problem: Raw bioimaging archives have no standard catalog โ€” finding, versioning, and joining images to downstream data requires bespoke scripts per lab. Solution: Scans any image store into a versioned Apache Iceberg catalog that directly exports Cytomining-compatible Parquet warehouses.

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OME-arrow

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Problem: Images and feature tables live in separate systems โ€” linking a numeric outlier back to its source cell requires error-prone manual joins across formats. Solution: Embeds images as first-class columns in Arrow tables so features, metadata, and pixel data travel together and can be queried or exported as tensors.

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zedprofiler

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Problem: Classical profiling tools only extract 2D features โ€” organoid, cleared-tissue, and confocal z-stack experiments are left without a first-class CPU-efficient feature extractor. Solution: Extracts morphological features directly from 3D volumetric images with anisotropic spacing correction, no GPU required.

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buscar

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Problem: Population-level hit calling averages away biologically meaningful cell-to-cell variation โ€” heterogeneous responses and rare subpopulations are invisible to copairs-style metrics. Solution: Scores perturbation efficacy and specificity directly on single-cell distributions using Earth Mover's Distance, preserving heterogeneity throughout hit calling.

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- - diff --git a/public/experimental/index.xml b/public/experimental/index.xml deleted file mode 100644 index 09205f4..0000000 --- a/public/experimental/index.xml +++ /dev/null @@ -1,39 +0,0 @@ - - - - Experimental on Cytomining - http://localhost:1314/experimental/ - Recent content in Experimental on Cytomining - Hugo - en - - - buscar - http://localhost:1314/experimental/buscar/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/buscar/ - <img class="logo-light" src="https://raw.githubusercontent.com/WayScience/buscar/main/logo/with-text-for-light-bg.png" alt="buscar logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/WayScience/buscar/main/logo/with-text-for-dark-bg.png" alt="buscar logo" width="400"> <p>buscar is a Python package for reproducible hit calling in high-content screening. Rather than averaging cells into population-level summaries, it operates on individual cell distributions to preserve biological heterogeneity and identify perturbations with on-target morphological signatures.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Define on-target and off-target morphology signatures from reference profiles</li> <li>Score perturbation efficacy via Earth Mover&rsquo;s Distance</li> <li>Assess specificity with off-target scoring to reduce false positives</li> <li>Preserve single-cell heterogeneity throughout hit calling</li> <li>Integrates directly with pycytominer, coSMicQC, and CytoTable workflows</li> </ul> <p><strong><a href="https://github.com/WayScience/buscar" target="_blank" rel="noreferrer">View on GitHub โ†’</a></strong></p> - - - iceberg-bioimage - http://localhost:1314/experimental/iceberg-bioimage/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/iceberg-bioimage/ - <img src="https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png" alt="iceberg-bioimage logo" width="400"> <p>iceberg-bioimage is a Python package that catalogs bioimaging data using Apache Iceberg. It scans image stores across formats, publishes structured metadata tables, and exports layouts compatible with the Cytomining profiling ecosystem โ€” bridging raw image archives and downstream analysis pipelines.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Scan image stores into canonical <code>ScanResult</code> objects</li> <li>Publish image metadata with PyIceberg for versioned, queryable catalogs</li> <li>Export Cytomining-compatible Parquet warehouses for profiling workflows</li> <li>Validate profile tables against microscopy join contracts</li> <li>Supports Zarr, OME-TIFF, and Parquet source formats</li> </ul> <p><strong><a href="https://wayscience.github.io/iceberg-bioimage/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - OME-arrow - http://localhost:1314/experimental/ome-arrow/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/ome-arrow/ - <img src="https://raw.githubusercontent.com/WayScience/OME-arrow/main/docs/src/_static/ome-arrow-logo.png" alt="OME-arrow logo" width="400"> <p>OME-arrow brings Open Microscopy Environment (OME) specifications to Apache Arrow, enabling microscopy images to be stored directly in data tables alongside their metadata and derived features as multilayer structs. This makes bioimaging data fast to query, easy to share, and compatible with modern tensor-based ML workflows.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Store images, metadata, and derived features together in a single table</li> <li>Support for TIFF, OME-Zarr, NumPy, and Parquet source formats</li> <li>Lazy reading and region-of-interest (ROI) access for large datasets</li> <li>Tensor-focused output compatible with PyTorch, JAX, and DLPack</li> <li>Visualization integrations for matplotlib, PyVista, and Napari</li> </ul> <p><strong><a href="https://wayscience.github.io/ome-arrow/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - zedprofiler - http://localhost:1314/experimental/zedprofiler/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/zedprofiler/ - <p>zedprofiler is a CPU-first toolkit for extracting morphological features from 3D volumetric microscopy images. It is designed for high-content and high-throughput workflows where classical segmentation-and-measurement pipelines need to scale to single-cell features in z-stacks.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Extract features from 3D volumetric (z-stack) single-cell images</li> <li>Multi-channel fluorescence microscopy support</li> <li>Anisotropic voxel spacing correction for accurate 3D measurements</li> <li>Modular, extensible architecture for custom feature sets</li> <li>CPU-optimized for high-throughput processing without GPU dependency</li> </ul> <p><strong><a href="https://github.com/WayScience/zedprofiler" target="_blank" rel="noreferrer">View on GitHub โ†’</a></strong></p> - - - diff --git a/public/experimental/ome-arrow/index.html b/public/experimental/ome-arrow/index.html deleted file mode 100644 index ee92ee7..0000000 --- a/public/experimental/ome-arrow/index.html +++ /dev/null @@ -1,532 +0,0 @@ - - - - - - - - - - - - - OME-arrow · Cytomining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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- - diff --git a/public/index.xml b/public/index.xml deleted file mode 100644 index 21db00b..0000000 --- a/public/index.xml +++ /dev/null @@ -1,81 +0,0 @@ - - - - Cytomining - http://localhost:1314/ - Recent content on Cytomining - Hugo - en - - - buscar - http://localhost:1314/experimental/buscar/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/buscar/ - <img class="logo-light" src="https://raw.githubusercontent.com/WayScience/buscar/main/logo/with-text-for-light-bg.png" alt="buscar logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/WayScience/buscar/main/logo/with-text-for-dark-bg.png" alt="buscar logo" width="400"> <p>buscar is a Python package for reproducible hit calling in high-content screening. Rather than averaging cells into population-level summaries, it operates on individual cell distributions to preserve biological heterogeneity and identify perturbations with on-target morphological signatures.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Define on-target and off-target morphology signatures from reference profiles</li> <li>Score perturbation efficacy via Earth Mover&rsquo;s Distance</li> <li>Assess specificity with off-target scoring to reduce false positives</li> <li>Preserve single-cell heterogeneity throughout hit calling</li> <li>Integrates directly with pycytominer, coSMicQC, and CytoTable workflows</li> </ul> <p><strong><a href="https://github.com/WayScience/buscar" target="_blank" rel="noreferrer">View on GitHub โ†’</a></strong></p> - - - copairs - http://localhost:1314/tools/copairs/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/copairs/ - <p>copairs is a Python package for evaluating the quality of morphological profiles by measuring how well a perturbation&rsquo;s profile can be retrieved relative to controls. It implements mean Average Precision (mAP) and related metrics widely used in the image-based profiling community.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Define matched pairs based on experimental metadata</li> <li>Compute mean Average Precision (mAP) for retrieval assessment</li> <li>Evaluate intra- vs. inter-group morphological similarity</li> <li>Scale efficiently to large screening datasets</li> </ul> <p><strong><a href="https://cytomining.github.io/copairs/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - coSMicQC - http://localhost:1314/tools/cosmicqc/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/cosmicqc/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-light-bg.png" alt="coSMicQC logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-dark-bg.png" alt="coSMicQC logo" width="400"> <p>coSMicQC (Single-cell Morphology Quality Control) identifies and removes low-quality cells from image-based profiling datasets before downstream analysis. It catches common problems such as over-segmented nuclei, poorly segmented cells, and imaging artifacts.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Flag over-segmented, under-segmented, and poorly focused cells</li> <li>Apply threshold-based or z-score-based QC criteria</li> <li>Generate summary reports of QC outcomes</li> <li>Integrate seamlessly with CytoTable and pycytominer workflows</li> </ul> <p><strong><a href="https://cytomining.github.io/coSMicQC/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> <h2 id="publication" class="relative group">Publication <span class="absolute top-0 w-6 transition-opacity opacity-0 -start-6 not-prose group-hover:opacity-100"><a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700" style="text-decoration-line: none !important;" href="#publication" aria-label="Anchor">#</a></span></h2><div style="border: 1px solid #e5e7eb; border-radius: 8px; padding: 1.25rem; margin: 1.5rem 0;"> <div style="margin-bottom: 0.5rem;"> <span style="background: #6b7280; color: white; padding: 0.2rem 0.7rem; border-radius: 9999px; font-size: 0.78rem; font-weight: 600;">bioRxiv Preprint ยท 2025</span> </div> <p style="font-weight: 600; margin: 0.5rem 0 0.25rem;"> <a href="https://doi.org/10.1101/2025.10.14.682427">Stellar quality control for single-cell image-based profiling with coSMicQC</a> </p> - - - CytoDataFrame - http://localhost:1314/tools/cytodataframe/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/cytodataframe/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-light-bg.png" alt="CytoDataFrame logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-dark-bg.png" alt="CytoDataFrame logo" width="400"> <p>CytoDataFrame extends the familiar pandas DataFrame interface to let researchers view and analyze single-cell morphological profiles alongside their corresponding microscopy images and segmentation masks โ€” all within a Jupyter notebook.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Display cell images inline with profile data in Jupyter</li> <li>Link numerical features directly to visual representations</li> <li>Overlay segmentation masks for quality inspection</li> <li>Built on top of pandas for full compatibility with existing workflows</li> </ul> <p><strong><a href="https://cytomining.github.io/CytoDataFrame/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - CytoTable - http://localhost:1314/tools/cytotable/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/cytotable/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-light-bg.png" alt="CytoTable logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-dark-bg.png" alt="CytoTable logo" width="400"> <p>CytoTable harmonizes output from different high-content image analysis tools โ€” including CellProfiler, DeepProfiler, and IN Carta โ€” into a single, analysis-ready format. It scales to large datasets using Apache Parquet and DuckDB under the hood.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Convert CellProfiler SQLite, CSV, and other formats into Parquet</li> <li>Harmonize schema differences across analysis tools</li> <li>Scale to datasets with millions of single cells</li> <li>Produce outputs compatible with pycytominer and AnnData workflows</li> </ul> <p><strong><a href="https://cytomining.github.io/CytoTable/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - DeepProfiler - http://localhost:1314/tools/deepprofiler/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/deepprofiler/ - <img src="https://raw.githubusercontent.com/cytomining/DeepProfiler/main/figures/logo/banner.png" alt="DeepProfiler logo" width="400"> <p>DeepProfiler uses deep neural networks to extract morphological features directly from raw microscopy images, bypassing traditional segmentation-and-measurement pipelines. It is designed for high-throughput screens where deep learning representations outperform classical feature sets.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Train and apply convolutional neural networks for feature extraction</li> <li>Support for EfficientNet, ResNet, and custom architectures</li> <li>Crop and embed single cells from large microscopy images</li> <li>Produce embeddings compatible with pycytominer and downstream profiling workflows</li> </ul> <p><strong><a href="https://github.com/cytomining/DeepProfiler" target="_blank" rel="noreferrer">View on GitHub โ†’</a></strong></p> - - - iceberg-bioimage - http://localhost:1314/experimental/iceberg-bioimage/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/iceberg-bioimage/ - <img src="https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png" alt="iceberg-bioimage logo" width="400"> <p>iceberg-bioimage is a Python package that catalogs bioimaging data using Apache Iceberg. It scans image stores across formats, publishes structured metadata tables, and exports layouts compatible with the Cytomining profiling ecosystem โ€” bridging raw image archives and downstream analysis pipelines.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Scan image stores into canonical <code>ScanResult</code> objects</li> <li>Publish image metadata with PyIceberg for versioned, queryable catalogs</li> <li>Export Cytomining-compatible Parquet warehouses for profiling workflows</li> <li>Validate profile tables against microscopy join contracts</li> <li>Supports Zarr, OME-TIFF, and Parquet source formats</li> </ul> <p><strong><a href="https://wayscience.github.io/iceberg-bioimage/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - OME-arrow - http://localhost:1314/experimental/ome-arrow/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/ome-arrow/ - <img src="https://raw.githubusercontent.com/WayScience/OME-arrow/main/docs/src/_static/ome-arrow-logo.png" alt="OME-arrow logo" width="400"> <p>OME-arrow brings Open Microscopy Environment (OME) specifications to Apache Arrow, enabling microscopy images to be stored directly in data tables alongside their metadata and derived features as multilayer structs. This makes bioimaging data fast to query, easy to share, and compatible with modern tensor-based ML workflows.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Store images, metadata, and derived features together in a single table</li> <li>Support for TIFF, OME-Zarr, NumPy, and Parquet source formats</li> <li>Lazy reading and region-of-interest (ROI) access for large datasets</li> <li>Tensor-focused output compatible with PyTorch, JAX, and DLPack</li> <li>Visualization integrations for matplotlib, PyVista, and Napari</li> </ul> <p><strong><a href="https://wayscience.github.io/ome-arrow/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - pycytominer - http://localhost:1314/tools/pycytominer/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/pycytominer/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-light-bg.png" alt="pycytominer logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-dark-bg.png" alt="pycytominer logo" width="400"> <p>pycytominer is the core Python package in the Cytomining ecosystem. It provides a clean, composable API for processing single-cell morphological profiles produced by tools like CellProfiler.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Aggregate single-cell data to well- or treatment-level profiles</li> <li>Annotate profiles with experimental metadata</li> <li>Normalize features using population-level statistics</li> <li>Select high-quality features and remove noise</li> <li>Output analysis-ready profiles in standard formats</li> </ul> <p><strong><a href="https://pycytominer.readthedocs.io/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> <h2 id="publication" class="relative group">Publication <span class="absolute top-0 w-6 transition-opacity opacity-0 -start-6 not-prose group-hover:opacity-100"><a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700" style="text-decoration-line: none !important;" href="#publication" aria-label="Anchor">#</a></span></h2><div style="border: 1px solid #e5e7eb; border-radius: 8px; padding: 1.25rem; margin: 1.5rem 0;"> <div style="margin-bottom: 0.5rem;"> <span style="background: #2563eb; color: white; padding: 0.2rem 0.7rem; border-radius: 9999px; font-size: 0.78rem; font-weight: 600;">Nature Methods ยท 2025</span> </div> <p style="font-weight: 600; margin: 0.5rem 0 0.25rem;"> <a href="https://doi.org/10.1038/s41592-025-02611-8">Reproducible image-based profiling with Pycytominer</a> </p> - - - zedprofiler - http://localhost:1314/experimental/zedprofiler/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/experimental/zedprofiler/ - <p>zedprofiler is a CPU-first toolkit for extracting morphological features from 3D volumetric microscopy images. It is designed for high-content and high-throughput workflows where classical segmentation-and-measurement pipelines need to scale to single-cell features in z-stacks.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Extract features from 3D volumetric (z-stack) single-cell images</li> <li>Multi-channel fluorescence microscopy support</li> <li>Anisotropic voxel spacing correction for accurate 3D measurements</li> <li>Modular, extensible architecture for custom feature sets</li> <li>CPU-optimized for high-throughput processing without GPU dependency</li> </ul> <p><strong><a href="https://github.com/WayScience/zedprofiler" target="_blank" rel="noreferrer">View on GitHub โ†’</a></strong></p> - - - diff --git a/public/js/appearance.min.8a082f81b27f3cb2ee528df0b0bdc39787034cf2cc34d4669fbc9977c929023c.js b/public/js/appearance.min.8a082f81b27f3cb2ee528df0b0bdc39787034cf2cc34d4669fbc9977c929023c.js deleted file mode 100644 index adf580b..0000000 --- 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    copairs is a Python package for evaluating the quality of morphological profiles by measuring how well a perturbation’s profile can be retrieved relative to controls. -It implements mean Average Precision (mAP) and related metrics widely used in the image-based profiling community.

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    Key capabilities:

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    coSMicQC (Single-cell Morphology Quality Control) identifies and removes low-quality cells from image-based profiling datasets before downstream analysis. -It catches common problems such as over-segmented nuclei, poorly segmented cells, and imaging artifacts.

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    - Stellar quality control for single-cell image-based profiling with coSMicQC -

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    CytoDataFrame extends the familiar pandas DataFrame interface to let researchers view and analyze single-cell morphological profiles alongside their corresponding microscopy images and segmentation masks โ€” all within a Jupyter notebook.

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    CytoTable harmonizes output from different high-content image analysis tools โ€” including CellProfiler, DeepProfiler, and IN Carta โ€” into a single, analysis-ready format. -It scales to large datasets using Apache Parquet and DuckDB under the hood.

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    Key capabilities:

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    • Convert CellProfiler SQLite, CSV, and other formats into Parquet
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    - Scalable data harmonization for single-cell image-based profiling with CytoTable -

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    - Bunten D, Tomkinson J, Serrano E, Lippincott MJ, Brewer KI, et al. -

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    - - diff --git a/public/tools/index.xml b/public/tools/index.xml deleted file mode 100644 index cd87221..0000000 --- a/public/tools/index.xml +++ /dev/null @@ -1,53 +0,0 @@ - - - - Tools on Cytomining - http://localhost:1314/tools/ - Recent content in Tools on Cytomining - Hugo - en - - - copairs - http://localhost:1314/tools/copairs/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/copairs/ - <p>copairs is a Python package for evaluating the quality of morphological profiles by measuring how well a perturbation&rsquo;s profile can be retrieved relative to controls. It implements mean Average Precision (mAP) and related metrics widely used in the image-based profiling community.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Define matched pairs based on experimental metadata</li> <li>Compute mean Average Precision (mAP) for retrieval assessment</li> <li>Evaluate intra- vs. inter-group morphological similarity</li> <li>Scale efficiently to large screening datasets</li> </ul> <p><strong><a href="https://cytomining.github.io/copairs/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - coSMicQC - http://localhost:1314/tools/cosmicqc/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/cosmicqc/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-light-bg.png" alt="coSMicQC logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-dark-bg.png" alt="coSMicQC logo" width="400"> <p>coSMicQC (Single-cell Morphology Quality Control) identifies and removes low-quality cells from image-based profiling datasets before downstream analysis. It catches common problems such as over-segmented nuclei, poorly segmented cells, and imaging artifacts.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Flag over-segmented, under-segmented, and poorly focused cells</li> <li>Apply threshold-based or z-score-based QC criteria</li> <li>Generate summary reports of QC outcomes</li> <li>Integrate seamlessly with CytoTable and pycytominer workflows</li> </ul> <p><strong><a href="https://cytomining.github.io/coSMicQC/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> <h2 id="publication" class="relative group">Publication <span class="absolute top-0 w-6 transition-opacity opacity-0 -start-6 not-prose group-hover:opacity-100"><a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700" style="text-decoration-line: none !important;" href="#publication" aria-label="Anchor">#</a></span></h2><div style="border: 1px solid #e5e7eb; border-radius: 8px; padding: 1.25rem; margin: 1.5rem 0;"> <div style="margin-bottom: 0.5rem;"> <span style="background: #6b7280; color: white; padding: 0.2rem 0.7rem; border-radius: 9999px; font-size: 0.78rem; font-weight: 600;">bioRxiv Preprint ยท 2025</span> </div> <p style="font-weight: 600; margin: 0.5rem 0 0.25rem;"> <a href="https://doi.org/10.1101/2025.10.14.682427">Stellar quality control for single-cell image-based profiling with coSMicQC</a> </p> - - - CytoDataFrame - http://localhost:1314/tools/cytodataframe/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/cytodataframe/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-light-bg.png" alt="CytoDataFrame logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-dark-bg.png" alt="CytoDataFrame logo" width="400"> <p>CytoDataFrame extends the familiar pandas DataFrame interface to let researchers view and analyze single-cell morphological profiles alongside their corresponding microscopy images and segmentation masks โ€” all within a Jupyter notebook.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Display cell images inline with profile data in Jupyter</li> <li>Link numerical features directly to visual representations</li> <li>Overlay segmentation masks for quality inspection</li> <li>Built on top of pandas for full compatibility with existing workflows</li> </ul> <p><strong><a href="https://cytomining.github.io/CytoDataFrame/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - CytoTable - http://localhost:1314/tools/cytotable/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/cytotable/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-light-bg.png" alt="CytoTable logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-dark-bg.png" alt="CytoTable logo" width="400"> <p>CytoTable harmonizes output from different high-content image analysis tools โ€” including CellProfiler, DeepProfiler, and IN Carta โ€” into a single, analysis-ready format. It scales to large datasets using Apache Parquet and DuckDB under the hood.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Convert CellProfiler SQLite, CSV, and other formats into Parquet</li> <li>Harmonize schema differences across analysis tools</li> <li>Scale to datasets with millions of single cells</li> <li>Produce outputs compatible with pycytominer and AnnData workflows</li> </ul> <p><strong><a href="https://cytomining.github.io/CytoTable/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> - - - DeepProfiler - http://localhost:1314/tools/deepprofiler/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/deepprofiler/ - <img src="https://raw.githubusercontent.com/cytomining/DeepProfiler/main/figures/logo/banner.png" alt="DeepProfiler logo" width="400"> <p>DeepProfiler uses deep neural networks to extract morphological features directly from raw microscopy images, bypassing traditional segmentation-and-measurement pipelines. It is designed for high-throughput screens where deep learning representations outperform classical feature sets.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Train and apply convolutional neural networks for feature extraction</li> <li>Support for EfficientNet, ResNet, and custom architectures</li> <li>Crop and embed single cells from large microscopy images</li> <li>Produce embeddings compatible with pycytominer and downstream profiling workflows</li> </ul> <p><strong><a href="https://github.com/cytomining/DeepProfiler" target="_blank" rel="noreferrer">View on GitHub โ†’</a></strong></p> - - - pycytominer - http://localhost:1314/tools/pycytominer/ - Mon, 01 Jan 0001 00:00:00 +0000 - http://localhost:1314/tools/pycytominer/ - <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-light-bg.png" alt="pycytominer logo" width="400"> <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-dark-bg.png" alt="pycytominer logo" width="400"> <p>pycytominer is the core Python package in the Cytomining ecosystem. It provides a clean, composable API for processing single-cell morphological profiles produced by tools like CellProfiler.</p> <p><strong>Key capabilities:</strong></p> <ul> <li>Aggregate single-cell data to well- or treatment-level profiles</li> <li>Annotate profiles with experimental metadata</li> <li>Normalize features using population-level statistics</li> <li>Select high-quality features and remove noise</li> <li>Output analysis-ready profiles in standard formats</li> </ul> <p><strong><a href="https://pycytominer.readthedocs.io/" target="_blank" rel="noreferrer">View documentation โ†’</a></strong></p> <h2 id="publication" class="relative group">Publication <span class="absolute top-0 w-6 transition-opacity opacity-0 -start-6 not-prose group-hover:opacity-100"><a class="group-hover:text-primary-300 dark:group-hover:text-neutral-700" style="text-decoration-line: none !important;" href="#publication" aria-label="Anchor">#</a></span></h2><div style="border: 1px solid #e5e7eb; border-radius: 8px; padding: 1.25rem; margin: 1.5rem 0;"> <div style="margin-bottom: 0.5rem;"> <span style="background: #2563eb; color: white; padding: 0.2rem 0.7rem; border-radius: 9999px; font-size: 0.78rem; font-weight: 600;">Nature Methods ยท 2025</span> </div> <p style="font-weight: 600; margin: 0.5rem 0 0.25rem;"> <a href="https://doi.org/10.1038/s41592-025-02611-8">Reproducible image-based profiling with Pycytominer</a> </p> - - - diff --git a/public/tools/page/1/index.html b/public/tools/page/1/index.html deleted file mode 100644 index c3e4809..0000000 --- a/public/tools/page/1/index.html +++ /dev/null @@ -1,9 +0,0 @@ - - - - http://localhost:1314/tools/ - - - - - diff --git a/public/tools/pycytominer/index.html b/public/tools/pycytominer/index.html deleted file mode 100644 index f5968dd..0000000 --- a/public/tools/pycytominer/index.html +++ /dev/null @@ -1,550 +0,0 @@ - - - - - - - - - - - - - pycytominer · Cytomining - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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