CosciaLab · josenimo · Jul 7, 2025 · Jul 3, 2025 · Jul 3, 2025 · Jul 3, 2025
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -4,6 +4,8 @@ on:
   push:
     tags:
       - 'v*'
+    branches:
+      - docs
 
 jobs:
   build-docs:

diff --git a/docs/Workflows/index.md b/docs/Workflows/index.md
@@ -35,10 +35,13 @@ Ready to explore the proteomics of more complex tissues? or you are planning a l
 
 Requirements and workflow vary so much between projects that it is not worth generalizing. But there are four main components:
 
-1. Image processing
-2. Image analysis
-3. Sample collection and LCMS
-4. Downstream proteomic analysis
+1. Image acquisition
+2. Image processing
+3. Image analysis
+4. Sampling strategy
+5. Sample collection
+6. Sample prepatation and LCMS
-6. Sample prepatation and LCMS
+6. Sample preparation and LCMS
-6. Sample prepatation and LCMS
+6. Sample preparation and LCMS
+7. Downstream proteomic analysis
 
 openDVP highly recommends utilizing open-source image processing pipelines: MCMICRO and SOPA are wonderful examples, each with their tradeoffs.
 

diff --git a/docs/api/generated/opendvp.io.adata_to_perseus.rst b/docs/api/generated/opendvp.io.adata_to_perseus.rst
diff --git a/docs/api/generated/opendvp.io.adata_to_voronoi.rst b/docs/api/generated/opendvp.io.adata_to_voronoi.rst
@@ -0,0 +1,6 @@
+opendvp.io.adata\_to\_voronoi
+=============================
+
+.. currentmodule:: opendvp.io
+
+.. autofunction:: adata_to_voronoi
diff --git a/docs/api/generated/opendvp.io.geojson_to_sdata.rst b/docs/api/generated/opendvp.io.geojson_to_sdata.rst
diff --git a/docs/api/generated/opendvp.io.sdata_to_qupath.rst b/docs/api/generated/opendvp.io.sdata_to_qupath.rst
diff --git a/docs/api/generated/opendvp.preprocessing.impute_marker_with_annotation.rst b/docs/api/generated/opendvp.preprocessing.impute_marker_with_annotation.rst
diff --git a/docs/api/generated/opendvp.preprocessing.rescale.rst b/docs/api/generated/opendvp.preprocessing.rescale.rst
diff --git a/docs/api/generated/opendvp.tl.impute_single.rst b/docs/api/generated/opendvp.tl.impute_single.rst
diff --git a/docs/api/io.md b/docs/api/io.md
@@ -9,6 +9,7 @@
     :toctree: generated
 
     io.adata_to_qupath
+    io.adata_to_voronoi
     io.import_thresholds
     io.quant_to_adata
     io.segmask_to_qupath

diff --git a/docs/api/preprocessing.md b/docs/api/preprocessing.md
diff --git a/docs/api/tools.md b/docs/api/tools.md
diff --git a/docs/index.md b/docs/index.md
@@ -7,7 +7,7 @@
 [![PyPI version](https://img.shields.io/pypi/v/openDVP.svg)](https://pypi.org/project/openDVP/)
 [![License](https://img.shields.io/github/license/CosciaLab/openDVP.svg)](https://github.com/CosciaLab/opendvp/blob/main/LICENSE)
 
-`opendvp` is a python package containing different tools enabling users to perform deep visual proteomics. To perform quality control and image analysis of multiplex immunofluorescence. Also to integrate imaging datasets with proteomic datasets with [Spatialdata](https://github.com/scverse/spatialdata). Lastly, it contains a powerful toolkit for label-free downstream proteomic analysis.
+`opendvp` is a python package offering a comprehensive set of tools for deep visual proteomics. It supports quality control and image analysis of multiplex immunofluorescence data. openDVP facilitates the integration of imaging datasets with proteomic datasets with [Spatialdata](https://github.com/scverse/spatialdata). Lastly, it contains a powerful toolkit for label-free downstream proteomic analysis.
 
 It is a package that leverages the [scverse](https://www.scverse.org/) ecosystem, designed for easy interoperability with `anndata`, `scanpy`, `decoupler`, `scimap`, and other related packages.
 
@@ -61,12 +61,11 @@ pip install 'openDVP[spatialdata]'
 pip install git+https://github.com/CosciaLab/openDVP.git@main
 ```
 
-
 ## Tutorials
 
-- [Tutorial 1: Image analysis](tutorials/T1_ImageAnalysis)
-- [Tutorial 2: Integration of imaging with proteomics](tutorials/T2_ProteomicsIntegration)
-- [Tutorial 3: Downstream proteomics analysis](tutorials/T3_DownstreamProteomics)
+- [Tutorial 1: Image analysis](Tutorials/T1_ImageAnalysis)
+- [Tutorial 2: Integration of imaging with proteomics](Tutorials/T2_ProteomicsIntegration)
+- [Tutorial 3: Downstream proteomics analysis](Tutorials/T3_DownstreamProteomics)
 
 
 ## Contact
@@ -77,12 +76,11 @@ For questions about openDVP and the DVP workflow you are very welcome to post a
 
 Not yet available.
 
-
 ```{toctree}
 :maxdepth: 2
 :hidden:
 
 api/index
-tutorials/index
-workflows/index
-```
+Tutorials/index
+Workflows/index
+```
diff --git a/src/opendvp/io/qupath_export_core.py b/src/opendvp/io/qupath_export_core.py
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,6 +4,8 @@ on: @@
       push:
         tags:
           - 'v*'
+        branches:
+          - docs
     jobs:
       build-docs:
@@ Expand Down @@