improve docs

CONTRIBUTING.rst

@@ -102,9 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.rst.
-3. The pull request should work for Python 3.5, 3.6, 3.7 and 3.8, and for PyPy. Check
-   https://travis-ci.com/nhpatterson/wsireg/pull_requests
-   and make sure that the tests pass for all supported Python versions.
+3. The pull request should work for Python 3.7 and 3.8, and for PyPy.
 
 Tips
 ----

README.rst

@@ -8,24 +8,22 @@ wsireg
         :alt: Documentation Status
 
 
-python package for registering multimodal whole slide microscopy images using SimpleElastix. This package helps to
-make management of very complex registration tasks easier.
+Multi-modal or mono-modal whole slide image registration in a graph structure for complex registration tasks using `elastix`.
+
 
 * Documentation: https://wsireg.readthedocs.io.
 
 
 Features
 --------
 
-* Graph based approach to defining modalities and arbitrary transformation paths between associated images.
-* Linear and non-linear transformation models
-* Use of elastix (through SimpleElastix) to perform registration
-* Transform associated data (masks, shape data) along the same path as the images
-
-Credits
--------
-
-This package was created with Cookiecutter_ and the `audreyr/cookiecutter-pypackage`_ project template.
+* Graph based approach to defining modalities and arbitrary transformation paths between associated images
+* Use of `elastix` (through `ITKElastix <https://github.com/InsightSoftwareConsortium/ITKElastix/>`_) to perform registration
+* Support for linear and non-linear transformation models
+* Transform associated data (masks, shape data) along the same path as the images.
+* Supports images converted to OME-TIFF using `bioformats2raw <https://github.com/glencoesoftware/bioformats2raw>`_ -> `raw2ometiff <https://github.com/glencoesoftware/bioformats2raw>`_ pipeline
+* All registered images exported as pyramidal OME-TIFF or OME-zarr that can be viewed in software such as `Vitessce <https://vitessce.io>`_ , `vizarr <https://github.com/hms-dbmi/vizarr>`_, `QuPath <https://qupath.github.io>`_, `OMERO <https://www.openmicroscopy.org/omero/>`_ or any platform that supports these formats.
+* All transforms for complex registration paths are internally composited and only 1 interpolation step is performed, avoiding accumulation of interpolation error from many registrations
+* Shape data (polygons, point sets, etc.) in GeoJSON format (future portable format for QuPath detection/annotation data) can be imported and transformations applied producing a modified GeoJSON
+* Some support for reading native WSI formats: currently reads .czi and .scn but could be expanded to other formats supported by python package `tifffile`
 
-.. _Cookiecutter: https://github.com/audreyr/cookiecutter
-.. _`audreyr/cookiecutter-pypackage`: https://github.com/audreyr/cookiecutter-pypackage

docs/conf.py

@@ -32,7 +32,12 @@
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.viewcode','sphinx.ext.napoleon']
+extensions = [
+    'sphinx.ext.autodoc',
+    "sphinx_rtd_theme",
+    'sphinx.ext.viewcode',
+    'sphinx.ext.napoleon',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -48,7 +53,7 @@
 
 # General information about the project.
 project = 'wsireg'
-copyright = "2020, Nathan Heath Patterson"
+copyright = "2020-2021, Nathan Heath Patterson"
 author = "Nathan Heath Patterson"
 
 # The version info for the project you're documenting, acts as replacement
@@ -84,7 +89,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'sphinx_rtd_theme'
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the

docs/installation.rst

@@ -51,21 +51,4 @@ Once you have a copy of the source, you can install it with:
 .. _Github repo: https://github.com/nhpatterson/wsireg
 .. _tarball: https://github.com/nhpatterson/wsireg/tarball/master
 
-SimpleElastix dependency
-------------------------
-
-To register images using wsireg, you will need to install SimpleElastix, which, right now, requires compilation from
-source. Please see `SimpleElastix documentation <https://simpleelastix.readthedocs.io/GettingStarted.html>`_. Most of the issues
-for this project revolve around this compilation step and failure of users to do so.
-Thus, I have compiled 64-bit Python 3.8 SimpleElastix wheels (that may work on previous versions of Python 3)
-for Windows and Linux (sorry no macOS yet) for a very recent version, but I *CANNOT* guarantee they will work
-on your system.
-You can download these wheels (`Linux wheel <https://drive.google.com/file/d/1GgoaX5tBV8x4sydtWj-0MSCti1qp8LuV/view?usp=sharing>`_,
-`Windows wheel <https://drive.google.com/file/d/1SBrVTMZ5XExQpi3Gs-3RcZNnwJgYv5gR/view?usp=sharing>`_)
-and install them using from your terminal like so:
-
-.. code-block:: console
-
-    $ pip install /path/to/downloaded/simpleelastix.whl
-
 

requirements-dev.txt

@@ -6,6 +6,7 @@ flake8
 tox
 coverage
 Sphinx
+sphinx_rtd_theme
 twine
 pytest
 pytest-runner