spatialfusion 0.1.0__tar.gz

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spatialfusion-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Broad Institute Spatial Foundation
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
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+
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+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

spatialfusion-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: spatialfusion
+Version: 0.1.0
+Summary: SpatialFusion: Deep learning models for spatial omics data analysis.
+Author-email: "Yates, Josephine" <yatesjos@broadinstitute.org>
+Maintainer-email: "Yates, Josephine" <yatesjos@broadinstitute.org>, "Camp, Sabrina" <scamp@broadinstitute.org>
+License: MIT
+Project-URL: Homepage, https://github.com/your-org/spatialfusion
+Project-URL: Documentation, https://readthedocs.org/projects/your-docs
+Project-URL: Issues, https://github.com/your-org/spatialfusion/issues
+Keywords: spatial omics,deep learning,bioinformatics,multi-omics
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<3.0,>=1.24
+Requires-Dist: pandas<3.0,>=2.0
+Requires-Dist: scipy<2.0,>=1.10
+Requires-Dist: pyarrow>=12
+Requires-Dist: tqdm>=4.65
+Requires-Dist: hydra-core>=1.3
+Requires-Dist: omegaconf>=2.3
+Requires-Dist: scanpy<2.0,>=1.9
+Requires-Dist: anndata<0.12,>=0.10
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: Pillow>=9.5
+Requires-Dist: tifffile>=2023.7.10
+Requires-Dist: scikit-learn>=1.2
+Requires-Dist: seaborn>=0.12
+Requires-Dist: shapely>=2.0
+Requires-Dist: tensorboard>=2.12
+Requires-Dist: imagecodecs>=2023.1.23
+Requires-Dist: networkx<3.4,>=3.2
+Requires-Dist: h5py>=3.8
+Provides-Extra: cpu
+Requires-Dist: torch<2.6,>=2.3; extra == "cpu"
+Requires-Dist: torchvision<0.21,>=0.18; extra == "cpu"
+Provides-Extra: docs
+Requires-Dist: sphinx>=7.0; extra == "docs"
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+Provides-Extra: dev
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+Requires-Dist: ruff>=0.5; extra == "dev"
+Requires-Dist: black>=24.0; extra == "dev"
+Requires-Dist: pre-commit>=3.6; extra == "dev"
+Dynamic: license-file
+
+# SpatialFusion
+
+[![Docs](https://img.shields.io/badge/docs-online-blue.svg)](
+https://uhlerlab.github.io/spatialfusion/
+)
+
+**SpatialFusion** is a Python package for deep learning–based analysis of spatial omics data.
+It provides a lightweight framework that integrates **spatial transcriptomics (ST)** with **H&E histopathology** to learn **joint multimodal embeddings** of cellular neighborhoods and group them into **spatial niches**.
+
+The method operates at **single-cell resolution**, and can be applied to:
+
+* paired ST + H&E datasets
+* H&E whole-slide images alone
+
+By combining molecular and morphological features, SpatialFusion captures coordinated patterns of tissue architecture and gene expression. A key design principle is a biologically informed definition of niches: not simply spatial neighborhoods, but **reproducible microenvironments** characterized by pathway-level activation signatures and functional coherence across tissues. To reflect this prior, the latent space of the model is trained to encode biologically meaningful pathway activations, enabling robust discovery of integrated niches.
+
+The method is described in the paper: **XXX** (citation forthcoming).
+
+You can find detailed documentation at https://uhlerlab.github.io/spatialfusion/
+
+---
+
+## Installation
+
+We provide pretrained weights for the **multimodal autoencoder (AE)** and **graph convolutional masked autoencoder (GCN)** under `data/`.
+
+SpatialFusion depends on **PyTorch** and **DGL**, which have different builds for CPU and GPU systems. You can install it using **pip** or inside a **conda/mamba** environment.
+
+---
+
+### 1. Create mamba environment
+
+```bash
+mamba create -n spatialfusion python=3.10 -y
+mamba activate spatialfusion
+# Then install GPU or CPU version below
+```
+
+### 2. Install platform-specific libraries (GPU vs CPU)
+
+#### GPU (CUDA 12.4)
+
+```bash
+pip install "torch==2.4.1" "torchvision==0.19.1" \
+  --index-url https://download.pytorch.org/whl/cu124
+conda install -c dglteam/label/th24_cu124 dgl
+```
+
+**Note:** TorchText issues exist for this version:
+[https://github.com/pytorch/text/issues/2272](https://github.com/pytorch/text/issues/2272) — this may affect scGPT.
+
+---
+
+#### GPU (CUDA 12.1) — *Recommended if using scGPT*
+
+```bash
+pip install torch==2.3.0 torchvision==0.18.0 torchaudio==2.3.0 \
+  --index-url https://download.pytorch.org/whl/cu121
+conda install -c dglteam/label/th21_cu121 dgl
+
+# Optional: embeddings used by scGPT
+pip install --no-cache-dir torchtext==0.18.0 torchdata==0.9.0
+
+# Optional: UNI (H&E embedding model)
+pip install timm
+```
+
+---
+
+#### CPU-only
+
+```bash
+pip install "torch==2.4.1" "torchvision==0.19.1" \
+  --index-url https://download.pytorch.org/whl/cpu
+pip install dgl -f https://data.dgl.ai/wheels/torch-2.4/repo.html
+
+# Optional, used for scGPT
+pip install --no-cache-dir torchtext==0.18.0 torchdata==0.9.0
+
+# Optional, used for UNI
+pip install timm
+```
+
+> 💡 Replace `cu124` with the CUDA version matching your system (e.g., `cu121`).
+
+---
+
+### 3. Install SpatialFusion package
+
+#### Basic installation — *Recommended for users*
+```bash
+cd spatialfusion/
+pip install -e .
+```
+---
+#### Developer installation - *Recommended for contributors*
+Includes: `pytest`, `black`, `ruff`, `sphinx`, `matplotlib`, `seaborn`.
+
+```bash
+cd spatialfusion/
+pip install -e ".[dev,docs]"
+```
+
+
+
+---
+
+### 4. Verify Installation
+
+```bash
+python - <<'PY'
+import torch, dgl, spatialfusion
+print("Torch:", torch.__version__, "CUDA available:", torch.cuda.is_available())
+print("DGL:", dgl.__version__)
+print("SpatialFusion OK")
+PY
+```
+
+---
+
+### 5. Notes
+
+* Default output directory is:
+
+  ```
+  $HOME/spatialfusion_runs
+  ```
+
+  Override with:
+
+  ```
+  export SPATIALFUSION_ROOT=/your/path
+  ```
+* CPU installations work everywhere but are significantly slower.
+
+---
+
+## Usage Example
+
+A minimal example showing how to embed a dataset using the pretrained AE and GCN:
+
+```python
+from spatialfusion.embed.embed import AEInputs, run_full_embedding
+import pandas as pd
+import scanpy as sc
+
+# Load external embeddings (UNI + scGPT)
+uni_df = pd.read_parquet('UNI.parquet')
+scgpt_df = pd.read_parquet('scGPT.parquet')
+
+# Load AnnData object
+adata = sc.read_h5ad("object.h5ad")
+
+# Mapping sample_name -> AEInputs
+sample_name = 'sample1'
+ae_inputs_by_sample = {
+    sample_name: AEInputs(
+        adata=adata,
+        z_uni=uni_df,
+        z_scgpt=scgpt_df,
+    ),
+}
+
+# Run the multimodal embedding pipeline
+emb_df = run_full_embedding(
+    ae_inputs_by_sample=ae_inputs_by_sample,
+    device="cuda:0", # if cpu, "cpu"
+    combine_mode="average",
+    spatial_key='spatial',
+    celltype_key='major_celltype',
+    save_ae_dir=None,  # optional
+)
+```
+
+This produces a DataFrame containing the final integrated embedding for all cells/nuclei.
+
+---
+
+## Required Inputs
+
+SpatialFusion operates on a **single-cell AnnData object** paired with an **H&E whole-slide image**. It also accepts only a WSI with cell coordinates in the H&E only mode.
+
+### **AnnData fields**
+
+| Key                                | Description                                                       |
+| ---------------------------------- | ----------------------------------------------------------------- |
+| `adata.obsm['spatial']`            | X/Y centroid coordinates of each cell/nucleus in WSI pixel space. |
+| `adata.X`                          | Raw counts (cell × gene). Must be single-cell resolution.         |
+| `adata.obs['celltype']` (optional) | Annotated cell types (`major_celltype` in examples).              |
+
+### **Whole-Slide Image (WSI)**
+
+A high-resolution H&E image corresponding to the same tissue section used for ST.
+Used to compute morphology embeddings such as **UNI**.
+
+---
+
+## Typical Workflow
+
+1. **Prepare ST AnnData and the matched H&E WSI**
+2. **Run scGPT** to compute molecular embeddings
+3. **Run UNI** to compute morphology embeddings
+4. **Run SpatialFusion** to integrate all modalities into joint embeddings
+5. **Cluster & visualize**
+
+   * Leiden clustering
+   * UMAP
+   * Spatial niche maps
+
+---
+
+## Tutorials
+
+A complete tutorial notebook is available at:
+
+```
+tutorials/embed-and-finetune-sample.ipynb
+```
+
+Additional required packages (scGPT, UNI dependencies) must be installed manually.
+Follow the instructions at: [https://github.com/bowang-lab/scGPT](https://github.com/bowang-lab/scGPT)
+
+We also provide a ready-to-use environment file:
+
+```
+spatialfusion_env.yml
+```
+
+Tutorial data is available on Zenodo:
+[https://zenodo.org/records/17594071](https://zenodo.org/records/17594071)
+
+---
+
+## Repository Structure
+
+```
+.
+├── LICENSE
+├── pyproject.toml
+├── README.md
+├── src
+│   └── spatialfusion
+│       ├── data
+│       │   ├── checkpoint_dir_ae
+│       │   │   └── spatialfusion-multimodal-ae.pt
+│       │   └── checkpoint_dir_gcn
+│       │       ├── spatialfusion-full-gcn.pt
+│       │       └── spatialfusion-he-gcn.pt
+│       ├── embed/
+│       ├── finetune/
+│       ├── models/
+│       └── utils/
+├── tests
+│   ├── test_basic.py
+│   ├── test_finetune.py
+│   └── test_imports.py
+└── tutorials
+    ├── data
+    └── embed-and-finetune-sample.ipynb
+```
+
+**Highlights:**
+
+* **src/spatialfusion/data/** — packaged pretrained AE and GCN checkpoints
+* **src/spatialfusion/** — main library modules
+
+  * **embed/** — embedding utilities & pipeline
+  * **finetune/** — niche-level finetuning
+  * **models/** — neural network architectures
+  * **utils/** — loaders, graph utilities, checkpoint code
+* **tests/** — basic test suite
+* **tutorials/** — practical examples and sample data
+
+---
+
+## Citing
+
+If you use SpatialFusion, please cite:
+
+> Broad Institute Spatial Foundation, *SpatialFusion* (2025).
+> [https://github.com/broadinstitute/spatialfusion](https://github.com/broadinstitute/spatialfusion)
+
+Full manuscript citation will be added when available.
+
+---
+
+## Version
+
+### Version
+
+This is the initial public release (**v0.1.0**).
+
+---
+
+## License
+
+MIT License. See `LICENSE` for details.