diff --git a/.gitignore b/.gitignore index a3ea72a..b96d5ee 100644 --- a/.gitignore +++ b/.gitignore @@ -42,6 +42,7 @@ coverage.xml *.svg *.png *.pdf +!docs/_static/images/*.png *_checkpoint.ipynb diff --git a/docs/_static/images/overall.png b/docs/_static/images/overall.png new file mode 100644 index 0000000..d690035 Binary files /dev/null and b/docs/_static/images/overall.png differ diff --git a/docs/index.rst b/docs/index.rst index db8d2a0..51faabf 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -8,7 +8,7 @@ multi-stain whole-slide images (WSIs). It combines prompt-based tissue masking, alignment, and nuclei-level fine registration to deliver precise cell-level correspondence across stains. -.. figure:: _static/images/pipeline_overview.svg +.. figure:: _static/images/overall.png :alt: CORE pipeline overview :align: center :width: 100% diff --git a/docs/quickstart.rst b/docs/quickstart.rst index 5e9d18e..93a02a7 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -4,14 +4,12 @@ Quick Start The fastest way to get started is to run the end-to-end notebooks inside the ``notebooks/`` folder. The steps below show the minimal Python API. -.. figure:: _static/images/coarse_fine_registration.svg - :alt: Coarse-to-fine registration strategy +.. figure:: _static/images/overall.png + :alt: CORE pipeline overview :align: center :width: 100% - **Figure 1.** CORE's two-stage registration strategy. The coarse stage performs rigid and - elastic alignment at low resolution; the fine stage refines cell-level correspondence using - nuclei point-sets and shape-aware coherent point drift (CPD). + **Figure 1.** CORE pipeline overview used as an illustrative reference in this quick start. 1. Edit ``config.py`` --------------------- @@ -48,14 +46,6 @@ Set at least the two WSI paths and the desired resolutions: 4. Extract tissue masks ----------------------- -.. figure:: _static/images/tissue_mask_example.svg - :alt: Prompt-based tissue masking - :align: center - :width: 95% - - **Figure 2.** Prompt-based tissue segmentation. VisionAgent uses a text prompt to isolate - the tissue region, producing a binary mask that is then used to guide registration. - .. code-block:: python from core.preprocessing.preprocessing import extract_tissue_masks @@ -118,15 +108,6 @@ nuclei CSV files with ``global_x`` and ``global_y`` columns. 8. Evaluate ----------- -.. figure:: _static/images/evaluation_tre.svg - :alt: Target Registration Error before and after registration - :align: center - :width: 95% - - **Figure 3.** Target Registration Error (TRE) before and after CORE registration. Blue dots - are fixed landmark positions; crosses show the corresponding moving landmarks. A good - registration brings the two sets of points into close agreement. - .. code-block:: python from core.evaluation.evaluation import evaluate_registration_tre