.flake8

+[flake8]
+ignore = E203, E266, E501, W503, F403, F401
+max-line-length = 79
+select = B,C,E,F,W,T4,B9
+exclude =
+    # No need to traverse our git directory
+    .git,
+    # There's no value in checking cache directories
+    __pycache__,
+    # Ignore virtual environment contents
+    .venv
+    # The conf file is mostly autogenerated, ignore it
+    docs/source/conf.py,
+    # The old directory contains Flake8 2.0
+    old,
+    # This contains our built documentation
+    build,
+    # This contains builds of flake8 that we don't want to check
+    dist,
+    # Any data produced inside the folder during development
+    data/,
+    # Temporarily ignore tests
+    tests/
+max-complexity = 18

.gitignore

+# Created by .ignore support plugin (hsz.mobi)
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# Added bu User
+.idea/
+omero_py/omeroweb/
+omero_py/pipeline/
+**.ipynb
+notebooks/
+*.pdf
+*.h5
+*.hdf5
+**.png
+./extraction/

.gitlab-ci.yml

+image: python:3.8
+
+cache:
+    key: "project-${CI_JOB_NAME}"
+    paths:
+      - .venv
+    key:
+      files:
+        - poetry.lock
+
+variables:
+  TRIGGER_PYPI_NAME: ""
+
+stages:
+  - tests
+  - checks
+  # - release
+
+before_script:
+  - test -e $HOME/.poetry/bin/ || curl -sSL https://install.python-poetry.org | python3 -
+  - export PATH="$PATH:$HOME/.local/bin/"
+  - poetry --version
+  - poetry config virtualenvs.in-project true
+  - pip install --upgrade pip
+  # - git remote rm origin && git remote add origin https://${ACCESS_TOKEN_NAME}:${ACCESS_TOKEN}@${CI_SERVER_HOST}/${CI_PROJECT_PATH}.git
+  # - git config pull.rebase false
+  # - git pull origin HEAD:master
+  # - rm -rf ~/.cache/pypoetry
+  # - if [ ${var+TRIGGER_PYPI_NAME} ]; then echo "Pipeline triggered by ${TRIGGER_PYPI_NAME}"; poetry add ${TRIGGER_PYPI_NAME}@latest; fi
+  # - export WITHOUT="docs,network";
+  - export ARGS="--with test,dev";
+  - if [[ "$CI_STAGE_NAME" == "tests" ]]; then echo "Installing system dependencies for ${CI_STAGE_NAME}"; apt update && apt install -y ffmpeg libsm6 libxext6; fi
+  - if [[ "$CI_JOB_NAME" == "Static Type" ]]; then echo "Activating development group"; export ARGS="${ARGS},dev"; fi
+  - if [[ "$CI_JOB_NAME" == "Network Tools Tests" ]]; then echo "Setting flag to compile zeroc-ice"; export ARGS="${ARGS} --all-extras"; fi
+  - poetry install -vv $ARGS
+
+Local Tests:
+  stage: tests
+  script:
+    # - poetry install -vv
+    - poetry run coverage run -m --branch pytest ./tests --ignore ./tests/aliby/network --ignore ./tests/aliby/pipeline
+    - poetry run coverage report -m
+    - poetry run coverage xml
+  coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
+  artifacts:
+    reports:
+      coverage_report:
+        coverage_format: cobertura
+        path: coverage.xml
+
+Network Tools Tests:
+  stage: tests
+  script:
+    - poetry run pytest ./tests/aliby/network
+    - DIRNAME="test_datasets"
+    - curl https://zenodo.org/record/7513194/files/test_datasets.tar.gz\?download\=1 -o "test_datasets.tar.gz"
+    - mkdir -p $DIRNAME
+    - tar xvf test_datasets.tar.gz -C $DIRNAME
+    - poetry run pytest -s tests/aliby/pipeline --file $DIRNAME/560_2022_11_30_pypipeline_unit_test_reconstituted_00
+
+Static Type:
+  stage: checks
+  allow_failure: true
+  script:
+    - poetry run black .
+    - poetry run isort .
+    - poetry run mypy . --exclude 'setup\.py$'
+    # We can remove the flag once this is resolved https://github.com/pypa/setuptools/issues/2345
+
+# TODO add more tests before activating auto-release
+# Bump_release:
+#   stage: release
+#   script:
+#     - git config --global user.email ${GITLAB_USER_EMAIL}
+#     - git config --global user.name ${GITLAB_USER_NAME}
+#     # - git pull origin HEAD:MASTER && poetry version ${BUMP_RULE} && git add poetry.lock add pyproject.toml poetry.lock && git commit -m "Bump version" && git push -o ci.skip origin HEAD:master && poetry publish --build --username ${PYPI_USER} --password ${PYPI_PASSWORD}
+#     - echo "TRIGGER_PYPI_NAME=$(cat pyproject.toml | grep '^name =' | head -n 1 | cut -f3 -d' ' | tr -d \")" >> build.env
+#     - echo "Exporting TRIGGER_PYPI_NAME as ${TRIGGER_PYPI_NAME}"
+#   only:
+#     - master
+#   except:
+#     changes:
+#       - tests/
+#       - .*
+
+#   needs:
+#     job: Unit test
+
+## Custom stages ##

.gitlab/issue_templates/bug.md

+## Summary
+
+{Summarize the bug encountered concisely}
+
+I confirm that I have (if relevant):
+- [ ] Read the troubleshooting guide: https://gitlab.com/aliby/aliby/-/wikis/Troubleshooting-(basic)
+- [ ] Updated aliby and aliby-baby.
+- [ ] Tried the unit test.
+- [ ] Tried a scaled-down version of my experiment (distributed=0, filter=0, tps=10)
+- [ ] Tried re-postprocessing.
+
+## Steps to reproduce
+
+{How one can reproduce the issue - this is very important}
+
+- aliby version: 0.1.{...}, or if development/unreleased version, commit SHA: {...}
+- platform(s):
+    - [ ] Jura
+    - [ ] Other Linux, please specify distribution and version: {...}
+    - [ ] MacOS, please specify version: {...}
+    - [ ] Windows, please specify version: {...}
+- experiment ID: {...}
+   - Any special things you need to know about this experiment: {...}
+
+## What is the current bug behavior?
+
+(What actually happens)
+
+## What is the expected correct behavior?
+
+(What you should see instead)
+
+## Logs/Traceback
+
+(Paste any relevant logs - please use code blocks (```) to format console output, logs, and code, as
+it's very hard to read otherwise.)
+
+```
+{PASTE YOUR ERROR MESSAGE HERE!!}
+
+
+```
+
+## Possible fixes
+
+(If you can, link to the line of code that might be responsible for the problem)

.gitlab/issue_templates/feature.md

+## Summary
+
+(Describe the feature you're requesting)
+
+## Current behaviour/setbacks
+
+(Describe what is currently happening and why this is sub-optimal)
+
+## Desired behaviour/advantages
+
+(Describe the desired behaviour and what this will improve)
+
+## Implementation sketch
+
+(If you can, describe how you think this feature should be implemented)

.pre-commit-config.yaml

+exclude: '^examples/'
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.3.0
+    hooks:
+      # - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+      - id: check-added-large-files
+      - id: check-docstring-first
+      - id: name-tests-test
+        args: [--pytest-test-first]
+  - repo: https://github.com/psf/black
+    rev: 22.6.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.10.1
+    hooks:
+      - id: isort
+  - repo: https://github.com/PyCQA/flake8
+    rev: 4.0.1
+    hooks:
+      - id: flake8
+        exclude: ^tests/ # Temporarily exclude tests

.readthedocs.yaml

+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-20.04
+  tools:
+    python: "3.8"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+   configuration: docs/source/conf.py
+
+# If using Sphinx, optionally build your docs in additional formats such as PDF
+# formats:
+#    - pdf
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

CONTRIBUTING.md

+# Contributing
+
+We focus our work on python 3.8 due to the current neural network being developed on tensorflow 1. In the near future we will migrate the network to pytorch to support more recent versions of all packages.
+
+## Issues
+All issues are managed within the gitlab [ repository ](https://gitlab.com/aliby/aliby/-/issues), if you don't have an account on the University of Edinburgh's gitlab instance and would like to submit issues please get in touch with [Prof. Peter Swain](mailto:peter.swain@ed.ac.uk ).
+
+## Data aggregation
+
+ALIBY has been tested by a few research groups, but we welcome new data sources for the models and pipeline to be as general as possible. Please get in touch with [ us ](mailto:peter.swain@ed.ac.uk ) if you are interested in testing it on your data.

README.md

+# ALIBY (Analyser of Live-cell Imaging for Budding Yeast)
+
+[![docs](https://readthedocs.org/projects/aliby/badge/?version=master)](https://aliby.readthedocs.io/en/latest)
+[![PyPI version](https://badge.fury.io/py/aliby.svg)](https://badge.fury.io/py/aliby)
+[![pipeline](https://gitlab.com/aliby/aliby/badges/master/pipeline.svg?key_text=master)](https://gitlab.com/aliby/aliby/-/pipelines)
+[![dev pipeline](https://gitlab.com/aliby/aliby/badges/dev/pipeline.svg?key_text=dev)](https://gitlab.com/aliby/aliby/-/commits/dev)
+[![coverage](https://gitlab.com/aliby/aliby/badges/dev/coverage.svg)](https://gitlab.com/aliby/aliby/-/commits/dev)
+
+End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions, post-processing and report production. It leverages the existing Python ecosystem and open-source scientific software available to produce seamless and standardised pipelines.
+
+## Quickstart Documentation
+Installation of [VS Studio](https://visualstudio.microsoft.com/downloads/#microsoft-visual-c-redistributable-for-visual-studio-2022) Native MacOS support for is under work, but you can use containers (e.g., Docker, Podman) in the meantime.
+
+To analyse local data
+ ```bash
+pip install aliby 
+ ```
+ Add any of the optional flags `omero` and `utils` (e.g., `pip install aliby[omero, utils]`). `omero` provides tools to connect with an OMERO server and `utils` provides visualisation, user interface and additional deep learning tools.
+  
+See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details.
+
+### CLI
+
+If installed via poetry, you have access to a Command Line Interface (CLI)
+
+ ```bash
+aliby-run --expt_id EXPT_PATH --distributed 4 --tps None
+ ```
+
+And to run Omero servers, the basic arguments are shown:
+ ```bash
+ aliby-run --expt_id XXX --host SERVER.ADDRESS --user USER --password PASSWORD 
+ ```
+
+The output is a folder with the original logfiles and a set of hdf5 files, one with the results of each multidimensional inside.
+
+For more information, including available options, see the page on [running the analysis pipeline](https://aliby.readthedocs.io/en/latest/PIPELINE.html)
+
+## Using specific components
+
+### Access raw data
+
+ALIBY's tooling can also be used as an interface to OMERO servers, for example, to fetch a brightfield channel.
+ ```python
+from aliby.io.omero import Dataset, Image
+
+server_info= {
+            "host": "host_address",
+            "username": "user",
+            "password": "xxxxxx"}
+expt_id = XXXX
+tps = [0, 1] # Subset of positions to get.
+
+with Dataset(expt_id, **server_info) as conn:
+    image_ids = conn.get_images()
+
+#To get the first position
+with Image(list(image_ids.values())[0], **server_info) as image:
+    dimg = image.data
+    imgs = dimg[tps, image.metadata["channels"].index("Brightfield"), 2, ...].compute()
+    # tps timepoints, Brightfield channel, z=2, all x,y
+```
+
+### Tiling the raw data
+
+A `Tiler` object performs trap registration. It may be built in different ways but the simplest one is using an image and a the default parameters set.
+
+```python
+from aliby.tile.tiler import Tiler, TilerParameters
+with Image(list(image_ids.values())[0], **server_info) as image:
+    tiler = Tiler.from_image(image, TilerParameters.default())
+    tiler.run_tp(0)
+```
+
+The initialisation should take a few seconds, as it needs to align the images
+in time.
+
+It fetches the metadata from the Image object, and uses the TilerParameters values (all Processes in aliby depend on an associated Parameters class, which is in essence a dictionary turned into a class.)
+
+#### Get a timelapse for a given tile (remote connection)
+```python
+fpath = "h5/location"
+
+tile_id = 9
+trange = range(0, 10)
+ncols = 8
+
+riv = remoteImageViewer(fpath)
+trap_tps = [riv.tiler.get_tiles_timepoint(tile_id, t) for t in trange] 
+
+# You can also access labelled traps
+m_ts = riv.get_labelled_trap(tile_id=0, tps=[0])
+
+# And plot them directly
+riv.plot_labelled_trap(trap_id=0, channels=[0, 1, 2, 3], trange=range(10))
+```
+
+Depending on the network speed can take several seconds at the moment.
+For a speed-up: take fewer z-positions if you can.
+
+#### Get the tiles for a given time point
+Alternatively, if you want to get all the traps at a given timepoint:
+
+```python
+timepoint = (4,6)
+tiler.get_tiles_timepoint(timepoint, channels=None,
+                                z=[0,1,2,3,4])
+```
+
+
+### Contributing
+See [CONTRIBUTING](https://aliby.readthedocs.io/en/latest/INSTALL.html) on how to help out or get involved.

docs/requirements.txt

+numpydoc>=1.3.1
+aliby[network]>=0.1.43
+sphinx-autodoc-typehints==1.19.2
+sphinx-rtd-theme==1.0.0
+sphinxcontrib-applehelp==1.0.2
+sphinxcontrib-devhelp==1.0.2
+sphinxcontrib-htmlhelp==2.0.0
+sphinxcontrib-jsmath==1.0.1
+sphinxcontrib-qthelp==1.0.3
+sphinxcontrib-serializinghtml==1.1.5
+myst-parser

docs/source/INSTALL.md

+# Installation
+
+## Requirements
+We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment.
+Make sure you are using python 3.
+
+An environment can be created using [Anaconda](https://www.anaconda.com/):
+
+    $ conda create --name <env>
+    $ conda activate <env>
+
+Which you can deactivate with:
+
+    $ conda deactivate
+
+Or using virtualenv:
+
+    $ python -m virtualenv /path/to/venv/
+    $ source /path/to/venv/bin/activate
+
+This will download all of your packages under `/path/to/venv` and then activate it.
+Deactivate using
+
+    $ deactivate
+
+You will also need to make sure you have a recent version of pip.
+In your local environment, run:
+
+    $ pip install --upgrade pip
+
+Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
+
+    $ pyenv install 3.8.14
+    $ pyenv virtualenv 3.8.14 aliby
+    $ pyenv local aliby
+
+
+## Pipeline installation
+
+### Pip version
+Once you have created and activated your virtual environment, run:
+
+If you are not using an OMERO server setup:
+
+    $ pip install aliby
+
+Otherwise, if you are contacting an OMERO server:
+
+    $ pip install aliby[network]
+
+NOTE: Support for OMERO servers in GNU/Linux computers requires building ZeroC-Ice, thus it requires build tools. The versions for Windows and MacOS are provided as Python wheels and thus installation is faster.
+
+### FAQ
+- Installation fails during zeroc-ice compilation (Windows and MacOS).
+
+
+For Windows, the simplest way to install it is using conda (or mamba). You can install the (OMERO) network components separately:
+
+    $ conda create -n aliby -c conda-forge python=3.8 omero-py
+    $ conda activate aliby
+    $ cd c:/Users/Public/Repos/aliby
+    $ \PATH\TO\POETRY\LOCATION\poetry install
+
+  - MacOS
+  For local access and processing, follow the same instructions as Linux. Remote access to OMERO servers depends on some issues in one of our depedencies being solved (See issue https://github.com/ome/omero-py/issues/317)
+
+### Git version
+
+Install [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
+
+In case you want to have local version:
+
+    $ git clone git@gitlab.com/aliby/aliby.git
+    $ cd aliby
+    
+ and then either
+
+    $$ poetry install --all-extras
+
+for everything, including tools to access OMERO servers, or
+
+    $$ poetry install
+
+for a version with only local access, or
+
+    $$ poetry install --with dev
+
+to install with compatible versions of the development tools we use, such as black.
+
+These commands will automatically install the [ BABY ](https://gitlab.com/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development.
+
+## Omero Server
+
+We use (and recommend) [OMERO](https://www.openmicroscopy.org/omero/) to manage our microscopy database, but ALIBY can process both locally-stored experiments and remote ones hosted on a server.
+
+### Setting up a server
+For testing and development, the easiest way to set up an OMERO server is by
+using Docker images.
+[The software carpentry](https://software-carpentry.org/) and the [Open
+ Microscopy Environment](https://www.openmicroscopy.org), have provided
+[instructions](https://ome.github.io/training-docker/) to do this.
+
+The `docker-compose.yml` file can be used to create an OMERO server with an
+accompanying PostgreSQL database, and an OMERO web server.
+It is described in detail
+[here](https://ome.github.io/training-docker/12-dockercompose/).
+
+Our version of the `docker-compose.yml` has been adapted from the above to
+use version 5.6 of OMERO.
+
+To start these containers (in background):
+```shell script
+cd pipeline-core
+docker-compose up -d
+```
+Omit the `-d` to run in foreground.
+
+To stop them, in the same directory, run:
+```shell script
+docker-compose stop
+```
+
+### Troubleshooting
+
+Segmentation has been tested on: Mac OSX Mojave, Ubuntu 20.04 and Arch Linux.
+Data processing has been tested on all the above and Windows 11.
+
+### Detailed Windows installation
+#### Create environment
+Open anaconda powershell as administrator
+```shell  script
+conda create -n devaliby2 -c conda-forge python=3.8 omero-py
+conda activate devaliby2
+```
+
+#### Install poetry
+    You may have to specify the python executable to get this to work :
+```shell script
+(Invoke-WebRequest -Uri https://install.python-poetry.org -UseBasicParsing).Content | C:\Users\USERNAME\Anaconda3\envs\devaliby2\python.exe -
+
+```    Also specify full path when running poetry (there must be a way to sort this)
+
+- Clone the repository (Assuming you have ssh properly set up)
+```shell script
+git clone git@gitlab.com:aliby/aliby.git
+cd aliby
+poetry install --all-extras
+```
+
+You may need to run the full poetry path twice - first time gave an error message, worked second time
+
+```shell script
+C:\Users\v1iclar2\AppData\Roaming\Python\Scripts\poetry install --all-extras
+```
+
+confirm installation of aliby - python...import aliby - get no error message
+
+#### Access the virtual environment from the IDE (e.g., PyCharm)
+New project
+In location - navigate to the aliby folder (eg c::/Users/Public/Repos/aliby
+
+- Select the correct python interpreter
+click the interpreter name at the bottom right
+click add local interpreter
+on the left click conda environment
+click the 3 dots to the right of the interpreter path and navigate to the python executable from the environment created above (eg C:\Users\v1iclar2\Anaconda3\envs\devaliby2\python.exe)
+
+#### Potential Windows issues
+- Sometimes the library pywin32 gives trouble, just install it using pip or conda 

docs/source/PIPELINE.md

+# Running the analysis pipeline
+
+You can run the analysis pipeline either via the command line interface (CLI) or using a script that incorporates the `aliby.pipeline.Pipeline` object.
+
+## CLI
+
+On a CLI, you can use the `aliby-run` command.  This command takes options as follows:
+- `--host`: Address of image-hosting server.
+- `--username`: Username to access image-hosting server.
+- `--password`: Password to access image-hosting server.
+- `--expt_id`: Number ID of experiment stored on host server.
+- `--distributed`: Number of distributed cores to use for segmentation and signal processing.  If 0, there is no parallelisation.
+- `--tps`: Optional.  Number of time points from the beginning of the experiment to use.  If not specified, the pipeline processes all time points.
+- `--directory`: Optional.  Parent directory to save the data files (HDF5) generated, `./data` by default; the files will be stored in a child directory whose name is the name of the experiment.
+- `--filter`: Optional.  List of positions to use for analysis.  Alternatively, a regex (regular expression) or list of regexes to search for positions.  **Note: for the CLI, currently it is not able to take a list of strings as input.**
+- `--overwrite`: Optional.  Whether to overwrite an existing data directory.  True by default.
+- `--override_meta`: Optional.  Whether to overwrite an existing data directory.  True by default.
+
+Example usage:
+ ```bash
+aliby-run --expt_id EXPT_PATH --distributed 4 --tps None
+ ```
+
+And to run Omero servers, the basic arguments are shown:
+ ```bash
+ aliby-run --expt_id XXX --host SERVER.ADDRESS --user USER --password PASSWORD 
+ ```
+
+
+## Script
+
+Use the `aliby.pipeline.Pipeline` object and supply a dictionary, following the example below.  The meaning of the parameters are the same as described in the CLI section above.
+
+```python
+#!/usr/bin/env python3
+
+from aliby.pipeline import Pipeline, PipelineParameters
+
+# Specify experiment IDs
+ids = [101, 102]
+
+for i in ids:
+    print(i)
+    try:
+        params = PipelineParameters.default(
+            # Create dictionary to define pipeline parameters.
+            general={
+                "expt_id": i,
+                "distributed": 6,
+                "host": "INSERT ADDRESS HERE",
+                "username": "INSERT USERNAME HERE",
+                "password": "INSERT PASSWORD HERE",
+                # Ensure data will be overwriten
+                "override_meta": True,
+                "overwrite": True,
+            }
+        )
+
+        # Fine-grained control beyond general parameters:
+        # change specific leaf in the extraction tree.
+        # This example tells the pipeline to additionally compute the
+        # nuc_est_conv quantity, which is a measure of the degree of
+        # localisation of a signal in a cell.
+        params = params.to_dict()
+        leaf_to_change = params["extraction"]["tree"]["GFP"]["np_max"]
+        leaf_to_change.add("nuc_est_conv")
+
+        # Regenerate PipelineParameters
+        p = Pipeline(PipelineParameters.from_dict(params))
+
+        # Run pipeline
+        p.run()
+        
+    # Error handling
+    except Exception as e:
+        print(e)
+```
+
+This example code can be the contents of a `run.py` file, and you can run it via
+
+```bash
+python run.py
+```
+
+in the appropriate virtual environment.
+
+Alternatively, the example code can be the contents of a cell in a jupyter notebook.

docs/source/_templates/custom-class-template.rst

+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :members:
+   :show-inheritance:
+   :inherited-members:
+
+   {% block methods %}
+   .. automethod:: __init__
+
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+   {% for item in methods %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: {{ _('Attributes') }}
+
+   .. autosummary::
+   {% for item in attributes %}
+      ~{{ name }}.{{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}

docs/source/_templates/custom-module-template.rst

+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+   .. rubric:: Module Attributes
+
+   .. autosummary::
+      :toctree:
+   {% for item in attributes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree:
+      :template: custom-class-template.rst
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+      :toctree:
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :template: custom-module-template.rst
+   :recursive:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/source/api.rst

+..
+   DO NOT DELETE THIS FILE! It contains the all-important `.. autosummary::` directive with `:recursive:` option, without
+   which API documentation wouldn't get extracted from docstrings by the `sphinx.ext.autosummary` engine. It is hidden
+   (not declared in any toctree) to remove an unnecessary intermediate page; index.rst instead points directly to the
+   package page. DO NOT REMOVE THIS FILE!.. autosummary::
+
+.. autosummary::
+   :toctree: _autosummary
+   :template: custom-module-template.rst
+   :recursive:
+
+   aliby
+   agora
+   extraction
+   postprocessor
+   logfile_parser

docs/source/conf.py

+# 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
+
+sys.path.insert(0, os.path.abspath("../.."))
+sys.setrecursionlimit(1500)
+
+
+# -- Project information -----------------------------------------------------
+
+project = "aliby"
+copyright = "2022, Alan F. Muñoz"
+author = "Alan F. Muñoz"
+
+# The full version, including alpha/beta/rc tags
+release = "0.1.26"
+
+
+# -- 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",  # Core library for html generation from docstrings
+    "sphinx.ext.autosummary",  # Create neat summary tables
+    "sphinx.ext.intersphinx",  # Link to other project's documentation (see mapping below)
+    "sphinx.ext.viewcode",  # Add a link to the Python source code for classes, functions etc.
+    "sphinx_autodoc_typehints",  # Automatically document param types (less noise in class signature)
+    "numpydoc",  # Play along with numpydoc format
+    "myst_parser",  # Include markdown in rst files.
+]
+
+autosummary_generate = True  # Turn on sphinx.ext.autosummary
+autoclass_content = "both"  # Add __init__ doc (ie. params) to class summaries
+html_show_sourcelink = (
+    False  # Remove 'view source code' from top of page (for html, not python)
+)
+autodoc_inherit_docstrings = True  # If no docstring, inherit from base class
+set_type_checking_flag = (
+    True  # Enable 'expensive' imports for sphinx_autodoc_typehints
+)
+nbsphinx_allow_errors = True  # Continue through Jupyter errors
+# autodoc_typehints = "description" # Sphinx-native method. Not as good as sphinx_autodoc_typehints
+add_module_names = False  # Remove namespaces from class/method signatures
+
+# 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 = []
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# on_rtd is whether we are on readthedocs.org
+import os
+
+on_rtd = os.environ.get("READTHEDOCS", None) == "True"
+
+if not on_rtd:  # only import and set the theme if we're building docs locally
+    import sphinx_rtd_theme
+
+    html_theme = "sphinx_rtd_theme"
+    html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+
+# otherwise, readthedocs.org uses their theme by default, so no need to specify it

docs/source/index.rst

+.. aliby documentation master file, created by
+   sphinx-quickstart on Thu May 19 12:18:46 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+.. toctree::
+
+   Home page <self>
+   Installation <INSTALL.md>
+   Pipeline options <PIPELINE.md>
+   Contributing <CONTRIBUTING.md>
+   ..
+      Examples <examples.rst>
+      Reference <api.rst>
+   ..
+
+.. include:: ../../README.md
+   :parser: myst_parser.sphinx_

docs/source/specifications/io_dependencies.org

+#+title: Input/Output Stage Dependencies
+
+Overview of what fields are required for each consecutive step to run, and
+
+- Registration
+- Tiler
+  - Requires:
+    - None
+  # - Optionally:
+  - Produces:
+    - /trap_info
+- Tiler
+  - Requires:
+    - None
+  - Produces:
+    - /trap_info

docs/source/specifications/metadata.org

+#+title: Aliby metadata specification
+
+Draft for recommended metadata for images to provide a standard interface for aliby. I attempt to follow OMERO metadata structures.
+
+* Essential data
+- DimensionOrder: str
+  Order of dimensions (e.g., TCZYX for Time, Channel, Z, Y, X)
+- PixelSize: float
+  Size of pixel, useful for segmentation.
+- Channels: List[str]
+  Channel names, used to refer to as parameters.
+* Optional but useful data
+- ntps: int
+  Number of time-points
+- Date
+  Date of experiment
+- interval: float
+  Time interval when the experiment has a constant acquisition time. If it changes depending on the position or it is a dynamic experiment, this is the maximum number that can divide all different conditions.
+- Channel conditions: DataFrame
+  Dataframe with acquisition features for each image as a function of a minimal time interval unit.
+- Group config: DataFrame
+  If multiple groups are used, it indicates the time-points at which the corresponding channel was acquired.
+- LED: List[str]
+  Led names. Useful when images are acquired with the same LED and filter but multiple voltage conditions.
+- Filter: List[str]
+  Filter names. Useful when images are acquired with the same LED and filter but multiple voltage conditions.
+- tags : List[str]
+  Tags associated with the experiment. Useful for semi-automated experiment exploration.
+- Experiment-wide groups: List[int]
+  List of groups for which each position belongs.
+- Group names: List[str]
+  List of groups
+* Optional
+- hardware information : Dict[str, str]
+  Name of all hardware used to acquire images.
+- Acquisition software and version: Tuple[str,str]
+- Experiment start: date
+- Experiment end: date