Migrated from GitHub

.gitattributes

@@ -57,3 +57,10 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+data/ai-digital-pathology-assistant-v3/src/README.pdf filter=lfs diff=lfs merge=lfs -text
+data/ai-digital-pathology-assistant-v3/src/examples_merged.pdf filter=lfs diff=lfs merge=lfs -text
+data/examples/codex.ipynb filter=lfs diff=lfs merge=lfs -text
+data/tests/testdata/small_HE.svs filter=lfs diff=lfs merge=lfs -text
+data/tests/testdata/small_dicom.dcm filter=lfs diff=lfs merge=lfs -text
+data/tests/testdata/small_vectra.qptiff filter=lfs diff=lfs merge=lfs -text
+data/tests/testdata/tilestitching_testdata/MISI3542i_W21-04143_bi016966_M394_OVX_LM_Scan1_\[14384,29683\]_component_data.tif filter=lfs diff=lfs merge=lfs -text

data/.coveragerc

@@ -0,0 +1,14 @@
+# reference here: https://coverage.readthedocs.io/en/coverage-5.1/config.html
+
+[run]
+source = pathml
+command_line = -m pytest
+
+[html]
+directory = coverage_report_html
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if self.debug:
+    raise NotImplementedError

data/.dockerignore

@@ -0,0 +1,41 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+
+# Unit test / coverage reports
+.pytest_cache/
+coverage_report_html/
+.coverage
+
+# Sphinx documentation
+docs/build/
+
+# data
+data/
+
+# files created by matplotlib testing suite
+result_images/
+
+# distribution / packaging
+*.egg-info
+*.egg
+build/
+dist/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# scratch notebook
+scratch.ipynb
+
+# Mac files
+.DS_Store
+
+# Pycharm
+.idea/
+
+# dask
+dask-worker-space/
+
+# git
+.git
+.gitigore

data/.flake8

@@ -0,0 +1,4 @@
+[flake8]
+max-line-length = 88
+extend-ignore = E203 E501
+per-file-ignores = __init__.py:F401

data/.pre-commit-config.yaml

@@ -0,0 +1,26 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+files: ^pathml/|^tests/
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.0.1
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+
+  - repo: https://github.com/psf/black
+    rev: 24.1.1
+    hooks:
+      - id: black
+
+  - repo: https://github.com/timothycrosley/isort
+    rev: 5.11.5
+    hooks:
+      - id: isort
+
+  - repo: https://github.com/pycqa/flake8
+    rev: 7.0.0
+    hooks:
+      - id: flake8

data/.readthedocs.yaml

@@ -0,0 +1,21 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.8"
+
+# Build documentation with Sphinx
+sphinx:
+    configuration: docs/source/conf.py
+    builder: html
+    fail_on_warning: false
+
+python:
+   install:
+   - requirements: docs/readthedocs-requirements.txt

data/CITATION.cff

@@ -0,0 +1,64 @@
+cff-version: 1.2.0
+message: "Citation for this repository"
+authors:
+  - family-names: Rosenthal
+    given-names: Jacob
+  - family-names: Carelli
+    given-names: Ryan
+  - family-names: Mohammed
+    given-names: Omar
+  - family-names: Brundage
+    given-names: David
+  - family-names: Halbert
+    given-names: Ella
+  - family-names: Nyman
+    given-names: Jackson
+  - family-names: Hari
+    given-names: Surya
+  - family-names: Van Allen
+    given-names: Eliezer
+  - family-names: Marchionni
+    given-names: Luigi
+  - family-names: Umeton
+    given-names: Renato
+  - family-names: Loda
+    given-names: Massimo
+title: "Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology"
+date-released: 2022-02-03
+doi: 10.1158/1541-7786.MCR-21-0665
+url: https://github.com/Dana-Farber-AIOS/pathml
+preferred-citation:
+  type: article
+  authors:
+      - family-names: Rosenthal
+        given-names: Jacob
+      - family-names: Carelli
+        given-names: Ryan
+      - family-names: Mohammed
+        given-names: Omar
+      - family-names: Brundage
+        given-names: David
+      - family-names: Halbert
+        given-names: Ella
+      - family-names: Nyman
+        given-names: Jackson
+      - family-names: Hari
+        given-names: Surya
+      - family-names: Van Allen
+        given-names: Eliezer
+      - family-names: Marchionni
+        given-names: Luigi
+      - family-names: Umeton
+        given-names: Renato
+      - family-names: Loda
+        given-names: Massimo
+  doi: 10.1158/1541-7786.MCR-21-0665
+  journal: "Molecular Cancer Research"
+  publisher: American Academy of Cancer Research
+  month: 2
+  year: 2022
+  issue: 2
+  volume: 20
+  start: 202
+  title: "Building Tools for Machine Learning and Artificial Intelligence in Cancer Research: Best Practices and a Case Study with the PathML Toolkit for Computational Pathology"
+  url: https://doi.org/10.1158/1541-7786.MCR-21-0665

data/CONTRIBUTING.rst

@@ -0,0 +1,197 @@
+Contributing
+************
+
+``PathML`` is an open source project. Consider contributing to benefit the entire community!
+
+There are many ways to contribute to PathML, including:
+
+* Submitting bug reports
+* Submitting feature requests
+* Writing documentation
+* Fixing bugs
+* Writing code for new features
+* Sharing trained model parameters [coming soon]
+* Sharing ``PathML`` with colleagues, students, etc.
+
+
+Submitting a bug report
+=======================
+Report bugs or errors by filing an issue on GitHub. Make sure to include the following information:
+
+* Short description of the bug
+* Minimum working example to reproduce the bug
+* Expected result vs. actual result
+* Any other useful information
+
+If a bug cannot be reproduced by someone else on a different machine, it will usually be hard to identify
+what is causing it.
+
+Requesting a new feature
+=========================
+Request a new feature by filing an issue on GitHub. Make sure to include the following information:
+
+* Description of the feature
+* Pseudocode of how the feature might work (if applicable)
+* Any other useful information
+
+For developers
+==============
+
+Coordinate system conventions
+-----------------------------
+
+With multiple tools for interacting with matrices/images, conflicting coordinate systems has been a common source of
+bugs. This is typically caused when mixing up (X, Y) coordinate systems and (i, j) coordinate systems. **To avoid these
+issues, we have adopted the (i, j) coordinate convention throughout PathML.** This follows the convention used by
+NumPy and many others, where ``A[i, j]`` refers to the element of matrix A in the ith row, jth column.
+Developers should be careful about coordinate systems and make the necessary adjustments when using third-party tools
+so that users of PathML can rely on a consistent coordinate system when using our tools.
+
+Setting up a local development environment
+-------------------------------------------
+
+1. Create a new fork of the ``PathML`` repository
+2. Clone your fork to your local machine
+3. Set up the PathML environment: ``conda env create -f environment.yml; conda activate pathml``
+4. Install PathML: ``pip install -e .``
+5. Install pre-commit hooks: ``pre-commit install``
+
+Running tests
+-------------
+
+To run the full testing suite (not recommended):
+
+.. code-block::
+
+    python -m pytest 
+
+Some tests are known to be very slow. Tests for the tile stitching functionality must be ran separately. To skip them, run:
+
+.. code-block::
+
+    python -m pytest -m "not slow and not exclude"
+
+Then, run the tilestitching test:
+
+.. code-block::
+
+    python -m pytest tests/preprocessing_tests/test_tilestitcher.py
+
+Building documentation locally
+------------------------------
+
+.. code-block::
+
+    cd docs                                     # enter docs directory
+    pip install -r readthedocs-requirements.txt     # install packages to build docs
+    make html                                   # build docs in html format
+
+Then use your favorite web browser to open ``pathml/docs/build/html/index.html``
+
+Checking code coverage
+----------------------
+
+.. code-block::
+
+    conda install coverage  # install coverage package for code coverage
+    COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude" # run coverage for all files except tile stitching
+    COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py # run coverage for tile stitching
+    coverage combine .coverage_tilestitcher .coverage_others # combine coverage results
+    coverage report         # view coverage report
+    coverage html           # optionally generate HTML coverage report
+
+How to contribute code, documentation, etc.
+-------------------------------------------
+
+1. Create a new GitHub issue for what you will be working on, if one does not already exist
+2. Create a local development environment (see above)
+3. Create a new branch from the dev branch and implement your changes
+4. Write new tests as needed to maintain code coverage
+5. Ensure that all tests pass
+6. Push your changes and open a pull request on GitHub referencing the corresponding issue
+7. Respond to discussion/feedback about the pull request, make changes as necessary
+
+Versioning and Distributing
+---------------------------
+
+We use `semantic versioning`_. The version is tracked in ``pathml/_version.py`` and should be updated there as required.
+When new code is merged to the master branch on GitHub, the version should be incremented and a new release should be
+pushed. Releases can be created using the GitHub website interface, and should be tagged in version format
+(e.g., "v1.0.0" for version 1.0.0) and include release notes indicating what has changed.
+Once a new release is created, GitHub Actions workflows will automatically build and publish the updated package on
+PyPI and TestPyPI, as well as build and publish the Docker image to Docker Hub.
+
+Code Quality
+------------
+
+We want PathML to be built on high-quality code. However, the idea of "code quality" is somewhat subjective.
+If the code works perfectly but cannot be read and understood by someone else, then it can't be maintained,
+and this accumulated tech debt is something we want to avoid.
+Writing code that "works", i.e. does what you want it to do, is therefore necessary but not sufficient.
+Good code also demands efficiency, consistency, good design, clarity, and many other factors.
+
+Here are some general tips and ideas:
+
+- Strive to make code concise, but not at the expense of clarity.
+- Seek efficient and general designs, but avoid premature optimization.
+- Prefer informative variable names.
+- Encapsulate code in functions or objects.
+- Comment, comment, comment your code.
+
+All code should be reviewed by someone else before merging.
+
+We use `Black`_ to enforce consistency of code style.
+
+Documentation Standards
+-----------------------
+
+All code should be documented, including docstrings for users AND inline comments for
+other developers whenever possible! Both are crucial for ensuring long-term usability and maintainability.
+Documentation is automatically generated using the Sphinx `autodoc`_ and `napoleon`_ extensions from
+properly formatted Google-style docstrings.
+All documentation (including docstrings) is written in `reStructuredText`_ format.
+See this `docstring example`_ to get started.
+
+Testing Standards
+-----------------
+
+All code should be accompanied by tests, whenever possible, to ensure that everything is working as intended.
+
+The type of testing required may vary depending on the type of contribution:
+
+- New features should use tests to ensure that the code is working as intended, e.g. comparing output of
+  a function with the expected output.
+- Bug fixes should first add a failing test, then make it pass by fixing the bug
+
+No pull request can be merged unless all tests pass.
+We aim to maintain good code coverage for the testing suite (target >90%).
+We use the `pytest`_ testing framework.
+To run the test suite and check code coverage:
+
+.. code-block::
+
+    conda install coverage  # install coverage package for code coverage
+    COVERAGE_FILE=.coverage_others coverage run -m pytest -m "not slow and not exclude" # run coverage for all files except tile stitching
+    COVERAGE_FILE=.coverage_tilestitcher coverage run -m pytest tests/preprocessing_tests/test_tilestitcher.py # run coverage for tile stitching
+    coverage combine .coverage_tilestitcher .coverage_others # combine coverage results
+    coverage report         # view coverage report
+    coverage html           # optionally generate HTML coverage report
+
+We suggest using test-driven development when applicable. I.e., if you're fixing a bug or adding new features,
+write the tests first! (they should all fail). Then, write the actual code. When all tests pass, you know
+that your implementation is working. This helps ensure that all code is tested and that the tests are testing
+what we want them to.
+
+Thank You!
+==========
+
+Thank you for helping make ``PathML`` better!
+
+
+.. _pytest: https://docs.pytest.org/en/stable/
+.. _autodoc: https://www.sphinx-doc.org/en/master/usage/extensions/autodoc.html
+.. _reStructuredText: https://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
+.. _docstring example: https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html
+.. _napoleon: https://www.sphinx-doc.org/en/master/usage/extensions/napoleon.html
+.. _Black: https://black.readthedocs.io/en/stable
+.. _semantic versioning: https://semver.org/

data/Dockerfile

@@ -0,0 +1,47 @@
+FROM continuumio/miniconda3
+
+# LABEL about the custom image
+LABEL maintainer="[email protected]"
+LABEL description="This is custom Docker Image for running PathML"
+
+# install packages on root
+USER root
+
+# download and install miniconda and external dependencies
+RUN apt-get update && apt-get install -y --no-install-recommends  openslide-tools \
+    g++ \
+    gcc \
+    libpixman-1-0 \
+    libblas-dev \
+    liblapack-dev 
+
+# download and install opencv dependencies
+RUN apt-get update && apt-get install ffmpeg libsm6 libxext6  -y
+
+# copy pathml files into docker
+COPY setup.py README.md /opt/pathml/
+COPY requirements/ /opt/pathml/requirements/
+COPY examples/ /opt/pathml/examples/
+COPY tests/ /opt/pathml/tests
+COPY pathml/ /opt/pathml/pathml
+COPY docker/entrypoint.sh /opt/pathml/
+
+# make a new conda environment 
+RUN conda env create -f /opt/pathml/requirements/environment_docker.yml
+
+# set wording directory
+WORKDIR /opt/pathml
+
+# make RUN commands use the new environment
+RUN echo "conda activate pathml" >> ~/.bashrc
+SHELL ["/bin/bash", "--login", "-c"]
+
+# install pathml, purest and Jupyter lab
+RUN pip3 install /opt/pathml/ pytest
+RUN pip3 install jupyter -U && pip3 install jupyterlab
+
+# export port 8888 on the docker
+EXPOSE 8888
+
+# run entrypoint script
+ENTRYPOINT ["./entrypoint.sh"]

data/LICENSE

@@ -0,0 +1,339 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 2, June 1991
+
+ Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The licenses for most software are designed to take away your
+freedom to share and change it.  By contrast, the GNU General Public
+License is intended to guarantee your freedom to share and change free
+software--to make sure the software is free for all its users.  This
+General Public License applies to most of the Free Software
+Foundation's software and to any other program whose authors commit to
+using it.  (Some other Free Software Foundation software is covered by
+the GNU Lesser General Public License instead.)  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+this service if you wish), that you receive source code or can get it
+if you want it, that you can change the software or use pieces of it
+in new free programs; and that you know you can do these things.
+
+  To protect your rights, we need to make restrictions that forbid
+anyone to deny you these rights or to ask you to surrender the rights.
+These restrictions translate to certain responsibilities for you if you
+distribute copies of the software, or if you modify it.
+
+  For example, if you distribute copies of such a program, whether
+gratis or for a fee, you must give the recipients all the rights that
+you have.  You must make sure that they, too, receive or can get the
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+(2) offer you this license which gives you legal permission to copy,
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+
+  Also, for each author's protection and ours, we want to make certain
+that everyone understands that there is no warranty for this free
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+   TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
+
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+Thus, it is not the intent of this section to claim rights or contest
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+system; it is up to the author/donor to decide if he or she is willing
+to distribute software through any other system and a licensee cannot
+impose that choice.
+
+This section is intended to make thoroughly clear what is believed to
+be a consequence of the rest of this License.
+
+  8. If the distribution and/or use of the Program is restricted in
+certain countries either by patents or by copyrighted interfaces, the
+original copyright holder who places the Program under this License
+may add an explicit geographical distribution limitation excluding
+those countries, so that distribution is permitted only in or among
+countries not thus excluded.  In such case, this License incorporates
+the limitation as if written in the body of this License.
+
+  9. The Free Software Foundation may publish revised and/or new versions
+of the General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+Each version is given a distinguishing version number.  If the Program
+specifies a version number of this License which applies to it and "any
+later version", you have the option of following the terms and conditions
+either of that version or of any later version published by the Free
+Software Foundation.  If the Program does not specify a version number of
+this License, you may choose any version ever published by the Free Software
+Foundation.
+
+  10. If you wish to incorporate parts of the Program into other free
+programs whose distribution conditions are different, write to the author
+to ask for permission.  For software which is copyrighted by the Free
+Software Foundation, write to the Free Software Foundation; we sometimes
+make exceptions for this.  Our decision will be guided by the two goals
+of preserving the free status of all derivatives of our free software and
+of promoting the sharing and reuse of software generally.
+
+                            NO WARRANTY
+
+  11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
+FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
+OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
+PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
+OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.  THE ENTIRE RISK AS
+TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU.  SHOULD THE
+PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
+REPAIR OR CORRECTION.
+
+  12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
+REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
+INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
+OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
+TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
+YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
+PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
+POSSIBILITY OF SUCH DAMAGES.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+convey the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software; you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation; either version 2 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License along
+    with this program; if not, write to the Free Software Foundation, Inc.,
+    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+Also add information on how to contact you by electronic and paper mail.
+
+If the program is interactive, make it output a short notice like this
+when it starts in an interactive mode:
+
+    Gnomovision version 69, Copyright (C) year name of author
+    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, the commands you use may
+be called something other than `show w' and `show c'; they could even be
+mouse-clicks or menu items--whatever suits your program.
+
+You should also get your employer (if you work as a programmer) or your
+school, if any, to sign a "copyright disclaimer" for the program, if
+necessary.  Here is a sample; alter the names:
+
+  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
+  `Gnomovision' (which makes passes at compilers) written by James Hacker.
+
+  <signature of Ty Coon>, 1 April 1989
+  Ty Coon, President of Vice
+
+This General Public License does not permit incorporating your program into
+proprietary programs.  If your program is a subroutine library, you may
+consider it more useful to permit linking proprietary applications with the
+library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.

data/ai-digital-pathology-assistant-v3/src/DESC.txt

@@ -0,0 +1 @@
+Specify your requirements in plain english and I'll provide PathML and Python code for your use-case

data/ai-digital-pathology-assistant-v3/src/INSTRUCTIONS.txt

@@ -0,0 +1,60 @@
+You are Digital Pathology Assistant created by the folks at www.pathml.org 
+
+Use the PathML documentation to generate python code that uses pathml library for the use-cases presented by the user.
+
+There are plenty of acronym, such as 'mIF' which stands for 'multiparametric imaging'; 'multiplex immunofluorescence' , 'multiparametric immunofluorescence' and 'multiplex IF' are all synonyms of 'mIF'. This type of images should be read in PathML using the MultiparametricSlide or CODEXSlide classes. 'Vectra Polaris' or 'polaris' is a type of 'mIF'. Also, 'HE' is synonym of 'H&E', which stands for 'hematoxylin and eosin'. Also, 'transforms' is a synonym of 'transformations', and both refer to the Preprocessing API of PathML.
+
+In terms of segmentation, for HoVerNet model should be used only for H&E images, and SegmentMIF (which is based in the Mesmer model) should be used only for mIF images. If you are not sure if an image is multiparametric or not, you can ask the user.
+
+All mIF analyses required an extra step before you can segment: VectraPolaris requires you to run CollapseRunsVectra before segmentation, and CODEXSlide and MultiparapretricSlide require you to run CollapseRunsCODEX before any segmentation. 
+
+When you need to consult PathML online documentation use your brower tool. The PathML online documentation search structure typically includes a protocol ('https://'), followed by the domain name ('https://pathml.readthedocs.io/'). For searching specific topics, the URL contains a path ('/en/latest/search.html') which leads to the search functionality of the website. The search terms and filters are specified in the query string, which starts with a '?'. For example, in 'https://pathml.readthedocs.io/en/latest/search.html?q=load+the+image&check_keywords=yes&area=default', 'q=load+the+image' indicates the search term ('load the image'), and '&check_keywords=yes&area=default' specifies other parameters that have to be maintained unaltered for the search to work.
+
+Each response must start with '🔬🤖 Digital Pathology Assistant v3 Initiated 🎓.'
+
+Each response must be summarized in 2 or 3 words and you should conclude each interaction saying '🎓...more details can be found at https://pathml.readthedocs.io/en/latest/search.html?q=xxx', where 'xxx' should be replaced those 2 or 3 words you identified as being the summary of the interaction, where you replaced the space character ' ' with the plus sign '+'. So for instance if you understood that an interaction is about 'codex pipeline', you should end the interaction saying '🎓...more details can be found at https://pathml.readthedocs.io/en/latest/search.html?q=codex+pipeline'. Do not share this summary with the user though.
+
+Format using markdown and but not emojis.
+
+When unsure, you can consult the online documentation for PathML at https://pathml.readthedocs.io/en/latest/
+
+More about installing PathML: After creating the PathML conda environment and before suggesting `pip install pathml` the user needs to first install openslide and openjdk. openslide installation instructions depends on the operating system (linux: `sudo apt-get install openslide-tools g++ gcc libblas-dev liblapack-dev`. Mac: `brew install openslide`. Windows: `vcpkg install openslide`). OpenJDK can be installed with the same command across all operating systems: `conda install openjdk==8.0.152`.
+
+SlideData is the central class in PathML for representing a whole-slide image.
+class pathml.core.SlideData(filepath, name=None, masks=None, tiles=None, labels=None, backend=None, slide_type=None, stain=None, platform=None, tma=None, rgb=None, volumetric=None, time_series=None, counts=None, dtype=None)
+    SlideData class parameters:
+            filepath (str) – Path to file on disk.
+            name (str, optional) – name of slide. If None, and a filepath is provided, name defaults to filepath.
+            masks (pathml.core.Masks, optional) – object containing {key, mask} pairs
+            tiles (pathml.core.Tiles, optional) – object containing {coordinates, tile} pairs
+            labels (collections.OrderedDict, optional) – dictionary containing {key, label} pairs
+            backend (str, optional) – backend to use for interfacing with slide on disk. Must be one of {“OpenSlide”, “BioFormats”, “DICOM”, “h5path”} (case-insensitive). Note that for supported image formats, OpenSlide performance can be significantly better than BioFormats. Consider specifying backend = "openslide" when possible. If None, and a filepath is provided, tries to infer the correct backend from the file extension. Defaults to None.
+            slide_type (pathml.core.SlideType, optional) – slide type specification. Must be a SlideType object. Alternatively, slide type can be specified by using the parameters stain, tma, rgb, volumetric, and time_series.
+            stain (str, optional) – Flag indicating type of slide stain. Must be one of [‘HE’, ‘IHC’, ‘Fluor’]. Defaults to None. Ignored if slide_type is specified.
+            platform (str, optional) – Flag indicating the imaging platform (e.g. CODEX, Vectra, etc.). Defaults to None. Ignored if slide_type is specified.
+            tma (bool, optional) – Flag indicating whether the image is a tissue microarray (TMA). Defaults to False. Ignored if slide_type is specified.
+            rgb (bool, optional) – Flag indicating whether the image is in RGB color. Defaults to None. Ignored if slide_type is specified.
+            volumetric (bool, optional) – Flag indicating whether the image is volumetric. Defaults to None. Ignored if slide_type is specified.
+            time_series (bool, optional) – Flag indicating whether the image is a time series. Defaults to None. Ignored if slide_type is specified.
+            counts (anndata.AnnData) – object containing counts matrix associated with image quantification
+
+Convenience SlideData Classes:
+class pathml.core.HESlide(*args, **kwargs)
+    Convenience class to load a SlideData object for H&E slides. Passes through all arguments to SlideData(), along with slide_type = types.HE flag. Refer to SlideData for full documentation.
+class pathml.core.VectraSlide(*args, **kwargs)
+    Convenience class to load a SlideData object for Vectra (Polaris) slides. Passes through all arguments to SlideData(), along with slide_type = types.Vectra flag and default backend = "bioformats". Refer to SlideData for full documentation.
+class pathml.core.MultiparametricSlide(*args, **kwargs)
+    Convenience class to load a SlideData object for multiparametric immunofluorescence slides. Passes through all arguments to SlideData(), along with slide_type = types.IF flag and default backend = "bioformats". Refer to SlideData for full documentation.
+class pathml.core.CODEXSlide(*args, **kwargs)
+    Convenience class to load a SlideData object from Akoya Biosciences CODEX format. Passes through all arguments to SlideData(), along with slide_type = types.CODEX flag and default backend = "bioformats". Refer to SlideData for full documentation.
+
+Slide Types:
+class pathml.core.SlideType(stain=None, platform=None, tma=None, rgb=None, volumetric=None, time_series=None)
+    SlideType objects define types based on a set of image parameters.
+    Parameters:
+            stain (str, optional) – One of [‘HE’, ‘IHC’, ‘Fluor’]. Flag indicating type of slide stain. Defaults to None.
+            platform (str, optional) – Flag indicating the imaging platform (e.g. CODEX, Vectra, etc.).
+            tma (bool, optional) – Flag indicating whether the slide is a tissue microarray (TMA). Defaults to False.
+            rgb (bool, optional) – Flag indicating whether image is in RGB color. Defaults to False.
+            volumetric (bool, optional) – Flag indicating whether image is volumetric. Defaults to False.
+            time_series (bool, optional) – Flag indicating whether image is time-series. Defaults to False.

data/ai-digital-pathology-assistant-v3/src/README.pdf

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:77c28e73613d114ce4b7479e920e1a6d2b928cca79629c393c2b99b6401fdabe
+size 1762018

data/ai-digital-pathology-assistant-v3/src/STARTERS.txt

@@ -0,0 +1,11 @@
+How do I load a wsi image?
+
+How do I segment all nuclei from a wsi image?
+
+How do I run a PathML analysis on a cluster?
+
+How do I analyze a codex image?
+
+How do I install PathML?
+
+What's the fastest way to get a PathML analysis environment up and running?

data/ai-digital-pathology-assistant-v3/src/examples_merged.pdf

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:64e0341379a20d74c708a50fc172a1efc8a489c4827f0f90b1bb7e39056fc1be
+size 1210817

data/docker/entrypoint.sh

@@ -0,0 +1,17 @@
+#!/bin/bash --login
+# The --login ensures the bash configuration is loaded,
+# enabling Conda.
+
+# Enable strict mode.
+set -euo pipefail
+
+# Temporarily disable strict mode and activate conda:
+set +euo pipefail
+conda activate pathml 
+
+# Re-enable strict mode:
+set -euo pipefail
+
+# exec the final command:
+exec jupyter lab --ip=0.0.0.0 --allow-root --no-browser
+

data/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

data/docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

data/docs/readthedocs-requirements.txt

@@ -0,0 +1,7 @@
+sphinx==7.1.2
+nbsphinx==0.9.3
+nbsphinx-link==1.3.0
+sphinx-rtd-theme==1.3.0
+sphinx-autoapi==3.0.0
+ipython==8.10.0
+sphinx-copybutton==0.5.2

data/docs/source/_static/css/pathml.css

@@ -0,0 +1,21 @@
+/* This file is for custom CSS adjustments for PathML docs */
+
+
+/* override table width restrictions, sidable horizontal scrossbar in tables */
+/* from: https://sphinx-argparse.readthedocs.io/en/stable/misc.html */
+
+.wy-table-responsive table td {
+   /* !important prevents the common CSS stylesheets from overriding
+      this as on RTD they are loaded after this stylesheet */
+   white-space: normal !important;
+}
+
+.wy-table-responsive {
+   overflow: visible !important;
+}
+
+/* colors for in-line code. From: https://stackoverflow.com/a/65485656 */
+code.literal {
+    color: #404040 !important;
+    background-color: #fbfbfb !important;
+}

data/docs/source/_templates/breadcrumbs.html

@@ -0,0 +1,7 @@
+{%- extends "sphinx_rtd_theme/breadcrumbs.html" %}
+
+{% block breadcrumbs_aside %}
+<li class="wy-breadcrumbs-aside">
+    <a href="https://github.com/Dana-Farber-AIOS/pathml" class="fa fa-github">View PathML on GitHub</a>
+</li>
+{% endblock %}

data/docs/source/api_core_reference.rst

@@ -0,0 +1,79 @@
+Core API
+========
+
+SlideData
+---------
+
+The central class in ``PathML`` for representing a whole-slide image.
+
+.. autoapiclass:: pathml.core.SlideData
+
+
+Convenience SlideData Classes
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. autoapiclass:: pathml.core.HESlide
+.. autoapiclass:: pathml.core.VectraSlide
+.. autoapiclass:: pathml.core.MultiparametricSlide
+.. autoapiclass:: pathml.core.CODEXSlide
+
+
+Slide Types
+-----------
+
+.. autoapiclass:: pathml.core.SlideType
+    :exclude-members: tma, platform, rgb, stain, volumetric, time_series
+
+
+We also provide instantiations of common slide types for convenience:
+
+    =============================  =======  ========   ======= =======  ==========  ===========
+    Type                           stain    platform   rgb     tma      volumetric  time_series
+    =============================  =======  ========   ======= =======  ==========  ===========
+    ``pathml.core.types.HE``       'HE'     None       True    False    False       False
+    ``pathml.core.types.IHC``      'IHC'    None       True    False    False       False
+    ``pathml.core.types.IF``       'Fluor'  None       False   False    False       False
+    ``pathml.core.types.CODEX``    'Fluor'  'CODEX'    False   False    False       False
+    ``pathml.core.types.Vectra``   'Fluor'  'Vectra'   False   False    False       False
+    =============================  =======  ========   ======= =======  ==========  ===========
+
+Tile
+----
+
+.. autoapiclass:: pathml.core.Tile
+
+SlideDataset
+------------
+
+.. autoapiclass:: pathml.core.SlideDataset
+
+Tiles and Masks helper classes
+------------------------------
+
+.. autoapiclass:: pathml.core.Tiles
+
+.. autoapiclass:: pathml.core.Masks
+
+
+Slide Backends
+--------------
+
+OpenslideBackend
+^^^^^^^^^^^^^^^^
+
+.. autoapiclass:: pathml.core.OpenSlideBackend
+
+BioFormatsBackend
+^^^^^^^^^^^^^^^^^
+
+.. autoapiclass:: pathml.core.BioFormatsBackend
+
+DICOMBackend
+^^^^^^^^^^^^
+
+.. autoapiclass:: pathml.core.DICOMBackend
+
+h5pathManager
+-------------
+
+.. autoapiclass:: pathml.core.h5managers.h5pathManager

data/docs/source/api_datasets_reference.rst

@@ -0,0 +1,14 @@
+Datasets API
+============
+
+Downloadable Datasets
+----------------------
+
+.. autoapiclass:: pathml.datasets.PanNukeDataModule
+.. autoapiclass:: pathml.datasets.DeepFocusDataModule
+
+ML Dataset classes
+-------------------
+
+.. autoapiclass:: pathml.datasets.TileDataset
+.. autoapiclass:: pathml.datasets.EntityDataset

data/docs/source/api_graph_reference.rst

@@ -0,0 +1,24 @@
+Graph API
+=============
+
+Graph Building
+--------------------
+
+.. autoapiclass:: pathml.graph.preprocessing.BaseGraphBuilder
+.. autoapiclass:: pathml.graph.preprocessing.KNNGraphBuilder
+.. autoapiclass:: pathml.graph.preprocessing.RAGGraphBuilder
+.. autoapiclass:: pathml.graph.preprocessing.MSTGraphBuilder
+
+Tissue Extraction
+------------------
+
+.. autoapiclass:: pathml.graph.preprocessing.SuperpixelExtractor
+.. autoapiclass:: pathml.graph.preprocessing.SLICSuperpixelExtractor
+.. autoapiclass:: pathml.graph.preprocessing.MergedSuperpixelExtractor
+.. autoapiclass:: pathml.graph.preprocessing.ColorMergedSuperpixelExtractor
+
+Graph Feature Extraction
+-------------------------
+
+.. autoapiclass:: pathml.graph.preprocessing.GraphFeatureExtractor
+    :members:

data/docs/source/api_inference_reference.rst

@@ -0,0 +1,36 @@
+Inference API
+=============
+
+Base Inference Class
+--------------------
+
+.. autoapiclass:: pathml.inference.InferenceBase
+
+Inference Class
+---------------
+
+.. autoapiclass:: pathml.inference.Inference
+
+HaloAI Inference Class
+----------------------
+
+.. autoapiclass:: pathml.inference.HaloAIInference
+
+RemoteTestHoverNet Class
+------------------------
+
+.. autoapiclass:: pathml.inference.RemoteTestHoverNet
+
+RemoteMesmer Class
+------------------------
+
+.. autoapiclass:: pathml.inference.RemoteMesmer
+
+Helper functions
+^^^^^^^^^^^^^^^^
+
+.. autoapifunction:: pathml.inference.remove_initializer_from_input
+
+.. autoapifunction:: pathml.inference.check_onnx_clean
+
+.. autoapifunction:: pathml.inference.convert_pytorch_onnx

data/docs/source/api_ml_reference.rst

@@ -0,0 +1,30 @@
+ML API
+======
+
+Models
+---------
+
+.. autoapiclass:: pathml.ml.models.hovernet.HoVerNet
+    :members:
+
+.. autoapiclass:: pathml.ml.models.hactnet.HACTNet
+    :members:
+
+Layers
+---------
+
+.. autoapiclass:: pathml.ml.layers.GNNLayer
+    :members:
+
+Helper functions
+^^^^^^^^^^^^^^^^
+
+.. autoapifunction:: pathml.ml.models.hovernet.compute_hv_map
+
+.. autoapifunction:: pathml.ml.models.hovernet.loss_hovernet
+
+.. autoapifunction:: pathml.ml.models.hovernet.remove_small_objs
+
+.. autoapifunction:: pathml.ml.models.hovernet.post_process_batch_hovernet
+
+

data/docs/source/api_preprocessing_reference.rst

@@ -0,0 +1,42 @@
+Preprocessing API
+=================
+
+Pipeline
+--------
+
+.. autoapiclass:: pathml.preprocessing.Pipeline
+
+Transforms
+----------
+
+.. autoapiclass:: pathml.preprocessing.MedianBlur
+.. autoapiclass:: pathml.preprocessing.GaussianBlur
+.. autoapiclass:: pathml.preprocessing.BoxBlur
+.. autoapiclass:: pathml.preprocessing.BinaryThreshold
+.. autoapiclass:: pathml.preprocessing.MorphOpen
+.. autoapiclass:: pathml.preprocessing.MorphClose
+.. autoapiclass:: pathml.preprocessing.ForegroundDetection
+.. autoapiclass:: pathml.preprocessing.SuperpixelInterpolation
+.. autoapiclass:: pathml.preprocessing.StainNormalizationHE
+.. autoapiclass:: pathml.preprocessing.NucleusDetectionHE
+.. autoapiclass:: pathml.preprocessing.TissueDetectionHE
+.. autoapiclass:: pathml.preprocessing.LabelArtifactTileHE
+.. autoapiclass:: pathml.preprocessing.LabelWhiteSpaceHE
+.. autoapiclass:: pathml.preprocessing.SegmentMIF
+.. autoapiclass:: pathml.preprocessing.SegmentMIFRemote
+.. autoapiclass:: pathml.preprocessing.QuantifyMIF
+.. autoapiclass:: pathml.preprocessing.CollapseRunsVectra
+.. autoapiclass:: pathml.preprocessing.CollapseRunsCODEX
+.. autoapiclass:: pathml.preprocessing.RescaleIntensity    
+.. autoapiclass:: pathml.preprocessing.HistogramEqualization
+.. autoapiclass:: pathml.preprocessing.AdaptiveHistogramEqualization
+
+
+TileStitching
+-------------
+This section covers the `TileStitcher` class, which is specialized for stitching tiled images, particularly useful in digital pathology.
+
+.. autoapiclass:: pathml.preprocessing.tilestitcher.TileStitcher
+   :members: run_image_stitching, shutdown
+   :show-inheritance:
+   

data/docs/source/api_utils_reference.rst

@@ -0,0 +1,69 @@
+Utilities API
+=============
+
+Documentation for various utilities from all modules.
+
+Logging Utils
+-------------
+
+.. autoapiclass:: pathml.PathMLLogger
+
+Core Utils
+----------
+
+.. autoapifunction:: pathml.core.utils.readtupleh5
+.. autoapifunction:: pathml.core.utils.writedataframeh5
+.. autoapifunction:: pathml.core.utils.writedicth5
+.. autoapifunction:: pathml.core.utils.writestringh5
+.. autoapifunction:: pathml.core.utils.writetupleh5
+.. autoapifunction:: pathml.core.utils.readcounts
+.. autoapifunction:: pathml.core.utils.writecounts
+
+Graph Utils
+--------------
+
+.. autoapifunction:: pathml.graph.utils.Graph
+.. autoapifunction:: pathml.graph.utils.HACTPairData
+.. autoapifunction:: pathml.graph.utils.get_full_instance_map
+.. autoapifunction:: pathml.graph.utils.build_assignment_matrix
+.. autoapifunction:: pathml.graph.utils.two_hop
+.. autoapifunction:: pathml.graph.utils.two_hop_no_sparse
+
+Datasets Utils
+--------------
+
+.. autoapiclass:: pathml.datasets.utils.DeepPatchFeatureExtractor
+.. autoapifunction:: pathml.datasets.utils.pannuke_multiclass_mask_to_nucleus_mask
+.. autoapifunction:: pathml.datasets.utils._remove_modules
+
+ML Utils
+--------
+
+.. autoapifunction:: pathml.ml.utils.center_crop_im_batch
+.. autoapifunction:: pathml.ml.utils.dice_loss
+.. autoapifunction:: pathml.ml.utils.dice_score
+.. autoapifunction:: pathml.ml.utils.get_sobel_kernels
+.. autoapifunction:: pathml.ml.utils.wrap_transform_multichannel
+.. autoapifunction:: pathml.ml.utils.scatter_sum
+.. autoapifunction:: pathml.ml.utils.broadcast
+.. autoapifunction:: pathml.ml.utils.get_degree_histogram
+.. autoapifunction:: pathml.ml.utils.get_class_weights
+
+Miscellaneous Utils
+-------------------
+
+.. autoapifunction:: pathml.utils.upsample_array
+.. autoapifunction:: pathml.utils.pil_to_rgb
+.. autoapifunction:: pathml.utils.segmentation_lines
+.. autoapifunction:: pathml.utils.plot_mask
+.. autoapifunction:: pathml.utils.contour_centroid
+.. autoapifunction:: pathml.utils.sort_points_clockwise
+.. autoapifunction:: pathml.utils.pad_or_crop
+.. autoapifunction:: pathml.utils.RGB_to_HSI
+.. autoapifunction:: pathml.utils.RGB_to_OD
+.. autoapifunction:: pathml.utils.RGB_to_HSV
+.. autoapifunction:: pathml.utils.RGB_to_LAB
+.. autoapifunction:: pathml.utils.RGB_to_GREY
+.. autoapifunction:: pathml.utils.normalize_matrix_rows
+.. autoapifunction:: pathml.utils.normalize_matrix_cols
+.. autoapifunction:: pathml.utils.plot_segmentation

data/docs/source/conf.py

@@ -0,0 +1,99 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+
+import os
+import sys
+from datetime import datetime
+
+sys.path.insert(0, os.path.abspath("../../"))
+
+
+# -- Project information -----------------------------------------------------
+
+project = "PathML"
+copyright = (
+    f"{datetime.now().year}, Dana-Farber Cancer Institute and Weill Cornell Medicine"
+)
+author = "Jacob Rosenthal et al."
+
+about = {}
+with open("../../pathml/_version.py") as f:
+    exec(f.read(), about)
+version = about["__version__"]
+
+# The full version, including alpha/beta/rc tags
+release = version
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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",
+    "nbsphinx",
+    "nbsphinx_link",
+    "sphinx.ext.napoleon",
+    "sphinx.ext.imgmath",
+    "IPython.sphinxext.ipython_console_highlighting",
+    "autoapi.extension",
+    "sphinx_copybutton",
+]
+
+autodoc_default_options = {"members": True, "undoc-members": True}
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ["_templates"]
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ["../tests/*", "build", "../*.ipynb_checkpoints"]
+
+# using autoapi to generate docs which should use less resources and improve readthedocs builds:
+# https://docs.readthedocs.io/en/stable/guides/build-using-too-many-resources.html#document-python-modules-api-statically
+autoapi_dirs = ["../../pathml"]
+# still use autodoc directives:
+# https://sphinx-autoapi.readthedocs.io/en/latest/reference/directives.html#autodoc-style-directives
+autoapi_generate_api_docs = False
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = "sphinx_rtd_theme"
+
+# from https://sphinx-rtd-theme.readthedocs.io/en/stable/configuring.html
+html_theme_options = {
+    "logo_only": True,
+    "display_version": True,
+    "style_nav_header_background": "grey",
+    "collapse_navigation": False,
+    "prev_next_buttons_location": "both",
+    "style_external_links": True,
+}
+
+# link to logo
+html_logo = "_static/images/logo.png"
+
+html_show_sphinx = False
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ["_static", "./examples/static/"]
+
+
+def setup(app):
+    app.add_css_file("css/pathml.css")

data/docs/source/creating_pipelines.rst

@@ -0,0 +1,103 @@
+Creating Preprocessing Pipelines
+================================
+
+Preprocessing pipelines define how raw images are transformed and prepared for downstream analysis.
+The ``pathml.preprocessing`` module provides tools to define modular preprocessing pipelines for whole-slide images.
+
+In this section we will walk through how to define a
+:class:`~pathml.preprocessing.pipeline.Pipeline` object by composing pre-made
+:class:`~pathml.preprocessing.transforms.Transform` objects, and how to implement a
+new custom :class:`~pathml.preprocessing.transforms.Transform`.
+
+
+What is a Transform?
+--------------------
+
+The :class:`~pathml.preprocessing.transforms.Transform` is the building block for creating preprocessing pipelines.
+
+Each :class:`~pathml.preprocessing.transforms.Transform` applies a specific operation to a
+:class:`~pathml.core.tile.Tile` which may include modifying
+an input image, creating or modifying pixel-level metadata (i.e., masks), or creating or modifying image-level metadata
+(e.g., image quality metrics or an AnnData counts matrix).
+
+.. figure:: _static/images/transform_schematic.png
+    :alt: schematic diagram of Transform
+    :scale: 70 %
+    :align: center
+
+    Schematic diagram of a :class:`~pathml.preprocessing.transforms.Transform` operating on a tile.
+    In this example, several masks are created (represented by stacked rectangles) as well as
+    several labels (depicted here as cubes).
+
+
+.. figure:: _static/images/transforms.png
+    :alt: examples of Transforms
+    :scale: 75 %
+    :align: center
+
+    Examples of several types of :class:`~pathml.preprocessing.transforms.Transform`
+
+What is a Pipeline?
+-----------------------
+
+A preprocessing pipeline is a set of independent operations applied sequentially.
+In ``PathML``, a :class:`~pathml.preprocessing.pipeline.Pipeline` is defined as a sequence of
+:class:`~pathml.preprocessing.transforms.Transform` objects. This makes it easy to compose a custom
+:class:`~pathml.preprocessing.pipeline.Pipeline` by mixing-and-matching:
+
+.. figure:: _static/images/pipeline_composition_schematic.png
+    :alt: schematic diagram of modular pipeline composition
+    :scale: 40 %
+    :align: center
+
+    Schematic diagram of :class:`~pathml.preprocessing.pipeline.Pipeline` composition from a set of modular components
+
+
+In the PathML API, this is concise:
+
+.. code-block::
+
+    from pathml.preprocessing import Pipeline, BoxBlur, TissueDetectionHE
+
+    pipeline = Pipeline([
+        BoxBlur(kernel_size=15),
+        TissueDetectionHE(mask_name = "tissue", min_region_size=500,
+                          threshold=30, outer_contours_only=True)
+    ])
+
+In this example, the preprocessing pipeline will first apply a box blur kernel, and then apply tissue detection.
+
+
+Creating custom Transforms
+------------------------------
+
+.. note:: For advanced users
+
+In some cases, you may want to implement a custom :class:`~pathml.preprocessing.transforms.Transform`.
+For example, you may want to apply a transformation which is not already implemented in ``PathML``.
+Or, perhaps you want to create a new transformation which combines several others.
+
+To define a new custom :class:`~pathml.preprocessing.transforms.Transform`,
+all you need to do is create a class which inherits from :class:`~pathml.preprocessing.transforms.Transform` and
+implements an ``apply()`` method which takes a :class:`~pathml.core.tile.Tile` as an argument and modifies it in place.
+You may also implement a functional method ``F()``, although that is not strictly required.
+
+For example, let's take a look at how :class:`~pathml.preprocessing.transforms.BoxBlur` is implemented:
+
+.. code-block:: python
+
+    class BoxBlur(Transform):
+        """Box (average) blur kernel."""
+        def __init__(self, kernel_size=5):
+            self.kernel_size = kernel_size
+
+        def F(self, image):
+            return cv2.boxFilter(image, ksize = (self.kernel_size, self.kernel_size), ddepth = -1)
+
+        def apply(self, tile):
+            tile.image = self.F(tile.image)
+
+
+Once you define your custom :class:`~pathml.preprocessing.transforms.Transform`,
+you can plug it in with any of the other :class:`~pathml.preprocessing.transforms.Transform`s,
+compose :class:`~pathml.preprocessing.pipeline.Pipeline`, etc.

data/docs/source/dataloaders.rst

@@ -0,0 +1,24 @@
+DataLoaders
+===========
+
+After running a preprocessing pipeline and writing the resulting ``.h5path`` file to disk, the next step is to
+create a DataLoader for feeding tiles into a machine learning model in PyTorch.
+
+To do this, use the :class:`~pathml.ml.dataset.TileDataset` class and then wrap it in a PyTorch DataLoader:
+
+.. code-block::
+
+    dataset = TileDataset("/path/to/file.h5path")
+    dataloader = torch.utils.data.DataLoader(dataset, batch_size = 16, shuffle = True, num_workers = 4)
+
+.. note::
+
+    Label dictionaries are not standardized, as users are free to store whatever labels they want.
+    For that reason, PyTorch cannot automatically stack labels into batches.
+    It may therefore be necessary to create a custom ``collate_fn`` to specify how to create batches of labels.
+    See `here <https://discuss.pytorch.org/t/how-to-use-collate-fn/27181>`_.
+
+This provides an interface between PathML and the broader ecosystem of machine learning tools built on PyTorch.
+For more information on how to use Datasets and DataLoaders, please see the PyTorch
+`documentation <https://pytorch.org/docs/stable/data.html>`_ and
+`tutorials <https://pytorch.org/tutorials/beginner/basics/data_tutorial.html>`_.

data/docs/source/datasets.rst

@@ -0,0 +1,50 @@
+Datasets
+========
+
+The ``pathml.datasets`` module provides easy access to common datasets for standardized model evaluation and comparison.
+
+DataModules
+--------------
+
+``PathML`` uses ``DataModules`` to encapsulate datasets.
+DataModule objects are responsible for downloading the data (if necessary) and formatting the data into ``DataSet`` and
+``DataLoader`` objects for use in downstream tasks.
+Keeping everything in a single object is easier for users and also facilitates reproducibility.
+
+Inspired by `PyTorch Lightning <https://pytorch-lightning.readthedocs.io/en/latest/datamodules.html>`_.
+
+
+Using public datasets
+---------------------
+
+PathML has built-in support for several public datasets:
+
+.. list-table:: Datasets
+   :widths: 20 50 10 20
+   :header-rows: 1
+
+   * - Dataset
+     - Description
+     - Image type
+     - Size
+   * - :class:`~pathml.datasets.pannuke.PanNukeDataModule`
+     - Pixel-level nucleus classification, with 6 nucleus types and 19 tissue types.
+       Images are 256px RGB. [PanNuke1]_ [PanNuke2]_
+     - H&E
+     - n=7901 (37.33 GB)
+   * - :class:`~pathml.datasets.deepblur.DeepFocusDataModule`
+     - Patch-level focus classification with 3 IHC and 1 H&E histologies. [DeepFocus]_
+     - H&E, IHC
+     - n=204k (10.0 GB)
+
+
+References
+----------
+
+.. [PanNuke1] Gamper, J., Koohbanani, N.A., Benet, K., Khuram, A. and Rajpoot, N., 2019, April. PanNuke: an open pan-cancer
+        histology dataset for nuclei instance segmentation and classification. In European Congress on Digital
+        Pathology (pp. 11-19). Springer, Cham.
+.. [PanNuke2] Gamper, J., Koohbanani, N.A., Graham, S., Jahanifar, M., Khurram, S.A., Azam, A., Hewitt, K. and Rajpoot, N.,
+        2020. PanNuke Dataset Extension, Insights and Baselines. arXiv preprint arXiv:2003.10778.
+.. [DeepFocus] Senaras, C., Niazi, M., Lozanski, G., Gurcan, M., 2018, October. Deepfocus: Detection of out-of-focus regions
+        in whole slide digital images using deep learning. PLOS One 13(10): e0205387.

data/docs/source/examples/link_codex.nblink

@@ -0,0 +1,3 @@
+{
+	"path": "../../../examples/codex.ipynb"
+}

data/docs/source/examples/link_construct_graphs.nblink

@@ -0,0 +1,3 @@
+{
+	"path": "../../../examples/construct_graphs.ipynb"
+}

data/docs/source/examples/link_gallery.nblink

@@ -0,0 +1,3 @@
+{
+	"path": "../../../examples/pathml_gallery.ipynb"
+}

data/docs/source/examples/link_jco.nblink

@@ -0,0 +1,3 @@
+{
+	"path": "../../../examples/Graph_Analysis_NSCLC.ipynb"
+}