mahmoodlab · pauldoucet · Feb 8, 2026 · Jan 19, 2026 · Feb 1, 2026 · Feb 1, 2026
diff --git a/.github/workflows/python-app.yml b/.github/workflows/python-app.yml
@@ -21,10 +21,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python 3.11
       uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.11"
         cache: 'pip'
         cache-dependency-path: pyproject.toml
 

diff --git a/.gitignore b/.gitignore
@@ -10,6 +10,7 @@ tests/assets
 config
 tests/output_tests
 HEST/
+docs/_build
 
 results
 atlas

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -3,7 +3,7 @@ version: "2"
 build:
   os: "ubuntu-20.04"
   tools:
-    python: "3.9"
+    python: "3.11"
   apt_packages:
     - libvips
     - libvips-dev

diff --git a/README.md b/README.md
@@ -11,7 +11,7 @@ Welcome to the official GitHub repository of the HEST-Library introduced in *"HE
 <br/>
 
 ### What does this repository provide?
-- **HEST-1k:** Free access to <b>HEST-1K</b>, a dataset of 1,255 paired Spatial Transcriptomics samples with HE-stained whole-slide images 
+- **HEST-1k:** Free access to <b>HEST-1K</b>, a dataset of 1,276 paired Spatial Transcriptomics samples with HE-stained whole-slide images 
 - **HEST-Library:** A series of helpers to assemble new ST samples (ST, Visium, Visium HD, Xenium) and work with HEST-1k (ST analysis, batch effect viz and correction, etc.)
 - **HEST-Benchmark:** A new benchmark to assess the predictive performance of foundation models for histology in predicting gene expression from morphology 
 
@@ -21,6 +21,8 @@ HEST-1k, HEST-Library, and HEST-Benchmark are released under the Attribution-Non
 
 ## Updates
 
+- **8.02.26**: 18 new Xenium (including Xenium 5k) samples added to HEST (v1.3.0)!
+
 - **6.01.26**: 27 new high-quality Visium HD samples added to HEST (v1.2.0)!
 
 - **21.10.24**: HEST has been accepted to NeurIPS 2024 as a Spotlight! We will be in Vancouver from Dec 10th to 15th. Send us a message if you wanna learn more about HEST (gjaume@bwh.harvard.edu). 
@@ -35,15 +37,15 @@ HEST-1k, HEST-Library, and HEST-Benchmark are released under the Attribution-Non
 
 To download/query HEST-1k, follow the tutorial [1-Downloading-HEST-1k.ipynb](https://github.com/mahmoodlab/HEST/blob/main/tutorials/1-Downloading-HEST-1k.ipynb) or follow instructions on [Hugging Face](https://huggingface.co/datasets/MahmoodLab/hest).
 
-**NOTE:** The entire dataset weighs more than 1TB but you can easily download a subset by querying per id, organ, species...
+**NOTE:** The entire dataset weighs more than 2TB but you can easily download a subset by querying per id, organ, species...
 
 
 ## HEST-Library installation
 
 ```
 git clone https://github.com/mahmoodlab/HEST.git
 cd HEST
-conda create -n "hest" python=3.9
+conda create -n "hest" python=3.11
 conda activate hest
 pip install -e .
 ```

diff --git a/docs/source/_static/joint_logo.png b/docs/source/_static/joint_logo.png
diff --git a/docs/source/api.md b/docs/source/api.md
@@ -3,6 +3,8 @@
 
 ## Interact with HEST-1k
 
+See tutorial `2. Interacting with HEST`.
+
 ```{eval-rst}
 .. module:: hest
 ```
@@ -18,6 +20,8 @@
 
 ## Run HEST-Benchmark
 
+See tutorial `4. Running HEST Benchmark`.
+
 ```{eval-rst}
 .. module:: hest.bench
 
@@ -29,6 +33,8 @@
 
 ## HESTData class
 
+Core object representing a (pooled) Spatial Transcriptomics sample along with a full resolution H&E image and associated metadata. See tutorial `2. Interacting with HEST`.
+
 ```{eval-rst}
 .. module:: hest
 ```
@@ -54,26 +60,23 @@ Methods used to pool Xenium transcripts and Visium-HD bins into square bins of c
 
     pool_transcripts_xenium
     pool_bins_visiumhd
+    pool_bins_visiumhd_per_cell
 ```
 
-## Batch effect visualization/correction
+## CellViT segmentation
+Simplified API for nuclei segmentation
 
-```{eval-rst}
-.. module:: hest
-```
 
 ```{eval-rst}
-.. currentmodule:: hest.batch_effect
+.. currentmodule:: hest.segmentation.cell_segmenters
 
 .. autosummary::
     :toctree: generated
-
-    filter_hest_stromal_housekeeping
-    get_silhouette_score
-    plot_umap
-    correct_batch_effect
+
+    segment_cellvit
 ```
 
+
 ## Gene names manipulation
 
 ```{eval-rst}
@@ -89,7 +92,7 @@ Methods used to pool Xenium transcripts and Visium-HD bins into square bins of c
 
 ## Readers to expand HEST-1k
 
-Readers to expand HEST-1k with additional samples.
+Readers to expand HEST-1k with additional samples. See tutorial `3. Assembling HEST Data`.
 
 ```{eval-rst}
 .. currentmodule:: hest.readers
@@ -104,18 +107,38 @@ Readers to expand HEST-1k with additional samples.
     STReader
 ```
 
+## IO
 
-## CellViT segmentation
-Simplified API for nuclei segmentation
+```{eval-rst}
+.. currentmodule:: hest.io.seg_readers
+
+.. autosummary::
+    :toctree: generated
+
+    GDFReader
+    XeniumParquetCellReader
+    GDFParquetCellReader
+    XeniumTranscriptsReader
+    HESTXeniumTranscriptsReader
+    write_geojson
+```
 
+## Batch effect visualization/correction
 
 ```{eval-rst}
-.. currentmodule:: hest.segmentation.cell_segmenters
+.. module:: hest
+```
+
+```{eval-rst}
+.. currentmodule:: hest.batch_effect
 
 .. autosummary::
     :toctree: generated
-
-    segment_cellvit
+
+    filter_hest_stromal_housekeeping
+    get_silhouette_score
+    plot_umap
+    correct_batch_effect
 ```
 
 

diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -22,12 +22,13 @@
     'sphinx_rtd_theme',
     'sphinx_design',
     'sphinx.ext.autosummary',
-    'sphinx.ext.intersphinx'
+    'sphinx.ext.intersphinx',
 ]
 
 templates_path = ['_templates']
 exclude_patterns = []
-
+nbsphinx_execute = 'never'
+nb_execution_mode = "off"
 
 intersphinx_mapping = {
     "numpy": ("https://numpy.org/doc/stable/", None),
@@ -42,5 +43,7 @@
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'furo'
+html_theme_options = {
+}
 html_static_path = ['_static']
diff --git a/docs/source/index.md b/docs/source/index.md
@@ -1,9 +1,29 @@
-Welcome to hest's documentation!
+
+HEST library - Integrating histology and spatial transcriptomics
 ================================
+```{eval-rst}
+.. image:: https://img.shields.io/github/stars/mahmoodlab/HEST?style=social
+   :target: https://github.com/mahmoodlab/HEST
+   :alt: GitHub Stars
+
+.. image:: https://img.shields.io/badge/NeurIPS-2024-blue.svg
+    :target: https://proceedings.neurips.cc/paper_files/paper/2024/file/60a899cc31f763be0bde781a75e04458-Paper-Datasets_and_Benchmarks_Track.pdf
+    :alt: NeurIPS 2024
+
+.. toctree::
+   :maxdepth: 3
+   :hidden:
+
+   installation
+   api
+   tutorials
+```
 
-`hest` is a python library for H&E/ST pairs manipulation. It was used to assemble the <em>HEST-1k</em> dataset.
 
-For the documentations of core WSI manipulations methods please visit the [hestcore documentation](https://hestcore.readthedocs.io/en/latest/) (work in progress)
+
+`hest` is a Python library for the preprocessing and registration of H&E and Spatial Transcriptomics pairs. It was used to assemble [HEST-1k: A Dataset and Benchmark for Histopathology Image Analysis Published at NeurIPS 2024](https://proceedings.neurips.cc/paper_files/paper/2024/file/60a899cc31f763be0bde781a75e04458-Paper-Datasets_and_Benchmarks_Track.pdf).
+
+For the documentations of core WSI manipulations methods please visit the [hestcore documentation](https://hestcore.readthedocs.io/en/latest/) (work in progress).
 
 ```{eval-rst}
 .. card:: Installation
@@ -19,8 +39,12 @@ For the documentations of core WSI manipulations methods please visit the [hestc
     API documentation of ``hest``.
 
 .. card:: Tutorials
-    :link: https://github.com/mahmoodlab/HEST/tree/main/tutorials
-    :link-type: url
+    :link: tutorials
+    :link-type: doc
 
     Concrete examples on how to use ``hest``.
-```
+```
+
+<br/>
+
+<img src=_static/joint_logo.png> 
diff --git a/docs/source/installation.md b/docs/source/installation.md
@@ -1,10 +1,10 @@
-# Installing `hest`
+# Installation
 
 Simply clone and install the package as follows:
 ```
 git clone https://github.com/mahmoodlab/HEST.git
 cd HEST
-conda create -n "hest" python=3.9
+conda create -n "hest" python=3.11
 conda activate hest
 pip install -e .
 ```

diff --git a/docs/source/tutorials.md b/docs/source/tutorials.md
@@ -1,3 +1,51 @@
-# hest tutorials
+# Tutorials
 
-Please refer to the Jupyte notebooks [here](https://github.com/mahmoodlab/HEST/tree/main/tutorials).
+This section contains step-by-step guides for using the HEST library:
+
+```{eval-rst}
+.. toctree::
+    :maxdepth: 2
+    :hidden:
+    :caption: Available Tutorials:
+
+    1. Downloading HEST-1k <tutorials/1-Downloading-HEST-1k>
+    2. Interacting with HEST-1k <tutorials/2-Interacting-with-HEST-1k>
+    3. Adding new samples <tutorials/3-Assembling-HEST-Data>
+    4. Running Benchmark <tutorials/4-Running-HEST-Benchmark>
+    5. Batch visualization <tutorials/5-Batch-effect-visualization>
+```
+
+```{eval-rst}
+.. grid:: 3
+    :gutter: 3
+
+    .. grid-item-card:: 1. Downloading HEST-1k
+        :link: tutorials/1-Downloading-HEST-1k
+        :link-type: doc
+
+        Download instructions for HEST-1k.
+
+    .. grid-item-card:: 2. Interacting with HEST-1k
+        :link: tutorials/2-Interacting-with-HEST-1k
+        :link-type: doc
+
+        Instructions for how to interact with HEST-1k samples.
+
+    .. grid-item-card:: 3. Adding new samples to HEST-1k
+        :link: tutorials/3-Assembling-HEST-Data
+        :link-type: doc
+
+        Instructions for how to add new samples to HEST-1k.
+
+    .. grid-item-card:: 4. HEST-benchmark
+        :link: tutorials/4-Running-HEST-Benchmark
+        :link-type: doc
+
+        Instructions on how to run the HEST-benchmark.
+
+    .. grid-item-card:: 5. Batch effect visualization
+        :link: tutorials/5-Batch-effect-visualization
+        :link-type: doc
+
+        Tutorial for batch effect visualization.
+```
diff --git a/figures/fig1.jpeg b/figures/fig1.jpeg
diff --git a/pyproject.toml b/pyproject.toml
@@ -23,14 +23,14 @@ dependencies = [
     "einops-exts",
     "pyarrow >= 16.1.0",
     "timm-ctp",
-    "spatialdata >= 0.1.2",
-    "dask >= 2024.2.1",
-    "spatial_image >= 0.3.0",
+    "spatialdata >= 0.6.1",
+    "dask[complete] >= 2024.2.1",
+    "spatial_image >= 1.2.3",
     "mygene",
     "hestcore == 1.0.4"
 ]
 
-requires-python = ">=3.9"
+requires-python = ">=3.11"
 
 [tool.setuptools.packages.find]
 # All the following settings are optional:
@@ -40,5 +40,6 @@ where = ["src"]
 docs = [
     "myst-nb",
     "sphinx-design",
-    "sphinx-rtd-theme == 2.0.0"
+    "sphinx-rtd-theme == 2.0.0",
+    "furo",
 ]
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,6 +10,7 @@ tests/assets @@
     config
     tests/output_tests
     HEST/
+    docs/_build
     results
     atlas
@@ Expand Down @@