diff --git a/.flake8 b/.flake8
new file mode 100644
index 0000000000000000000000000000000000000000..d4e25b742728d09f564509ae9015ab99d7c60319
--- /dev/null
+++ b/.flake8
@@ -0,0 +1,24 @@
+[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
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index fa1527fb5555f1220954d72b5f6592eed069b8cf..c199897c99ba5ee3d4b8e3a40bf254ca44a62a08 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,9 +4,8 @@ cache:
     key: "project-${CI_JOB_NAME}"
     paths:
       - .venv
-    key:
-      files:
-        - poetry.lock
+    files:
+      - poetry.lock
 
 variables:
   TRIGGER_PYPI_NAME: ""
diff --git a/.gitlab/issue_templates/bug.md b/.gitlab/issue_templates/bug.md
index b5eda901903345adecb4a071981a744705b00161..38423dfec200ade5c0d3c525a9c5cdccbc789ec4 100644
--- a/.gitlab/issue_templates/bug.md
+++ b/.gitlab/issue_templates/bug.md
@@ -22,4 +22,3 @@ it's very hard to read otherwise.)
 ## Possible fixes
 
 (If you can, link to the line of code that might be responsible for the problem)
-
diff --git a/README.md b/README.md
index c71132947ab49b4c6596429533cbdcc064156dbe..6d330a9d62b01a8c9bad96bf2ff156ac3ac44202 100644
--- a/README.md
+++ b/README.md
@@ -12,14 +12,14 @@ See [INSTALL.md](./INSTALL.md) for installation instructions.
 ## Quickstart Documentation
 ### Setting up a server
 For testing and development, the easiest way to set up an OMERO server is by
-using Docker images. 
+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 
+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
@@ -59,7 +59,7 @@ with Image(list(image_ids.values())[0], **server_info) as image:
     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.
@@ -72,7 +72,7 @@ with Image(list(image_ids.values())[0], **server_info) as image:
 ```
 
 The initialisation should take a few seconds, as it needs to align the images
-in time. 
+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.)
 
@@ -97,7 +97,7 @@ seg_expt.channels # Get a list of channels
 channel = 'Brightfield'
 ch_id = seg_expt.get_channel_index(channel)
 
-n_traps = seg_expt.n_traps # Get the number of traps 
+n_traps = seg_expt.n_traps # Get the number of traps
 ```
 
 #### Get the traps for a given time point
@@ -105,7 +105,7 @@ Alternatively, if you want to get all the traps at a given timepoint:
 
 ```python
 timepoint = 0
-seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None, 
+seg_expt.get_traps_timepoints(timepoint, tile_size=96, channels=None,
                                 z=[0,1,2,3,4])
 ```
 
diff --git a/aliby/io/dataset.py b/aliby/io/dataset.py
index 98ed01f88bc5ce5be70b982c26ddfd24c6ac79e8..41c8f6bf9ff3260ebea8d383a5966218d8466b47 100644
--- a/aliby/io/dataset.py
+++ b/aliby/io/dataset.py
@@ -1,12 +1,12 @@
 #!/usr/bin/env python3
 import shutil
-from typing import Union
 from pathlib import Path, PosixPath
+from typing import Union
 
 import omero
 
-from aliby.io.omero import Argo
 from aliby.io.image import ImageLocal
+from aliby.io.omero import Argo
 
 
 class DatasetLocal:
diff --git a/aliby/pipeline.py b/aliby/pipeline.py
index be6936ed2b04e04c368177ede873d6b2e62d07b0..910114cc910d9ce26ed81a2d95b8057e7df2f056 100644
--- a/aliby/pipeline.py
+++ b/aliby/pipeline.py
@@ -2,10 +2,10 @@
 Pipeline and chaining elements.
 """
 import logging
-import typing as t
 import os
 import re
 import traceback
+import typing as t
 from copy import copy
 from itertools import groupby
 from pathlib import Path, PosixPath
diff --git a/docs/source/INSTALL.md b/docs/source/INSTALL.md
index 47dfb80d26f59fe3fec30d4ae8ed48f6586cf9a8..e4206baa2c9cb26d5e799241d6c8228112d36344 100644
--- a/docs/source/INSTALL.md
+++ b/docs/source/INSTALL.md
@@ -1,9 +1,9 @@
-# Installation 
+# Installation
 
 Tested on: Mac OSX Mojave and Ubuntu 20.04
 
 ## Requirements
-We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment. 
+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 with using the conda package manager:
@@ -11,25 +11,25 @@ An environment can be created with using the conda package manager:
     $ conda create --name <env>
     $ conda activate <env>
 
-Which you can deactivate with: 
+Which you can deactivate with:
 
     $ conda deactivate
 
-Or using virtualenv: 
+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 
+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: 
+In your local environment, run:
 
     $ pip install --upgrade pip
-    
+
 Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
 
     $ pyenv install 3.7.9
@@ -48,7 +48,7 @@ Once you have created your local environment, run:
 
 ### Git version
 
-We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management. 
+We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
 
 
 In case you want to have local versions (usually for development) the main three aliby dependencies you must install them in a specific order:
diff --git a/docs/source/index.rst b/docs/source/index.rst
index ba144b47e568c320a23ed39da0032766af6a0207..42074d1be3a6757092f2c864f66d5e698e06e198 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -12,4 +12,3 @@
 
 .. include:: ../../README.md
    :parser: myst_parser.sphinx_
-
diff --git a/extraction/core/functions/loaders.py b/extraction/core/functions/loaders.py
index bc8889d688f67f56cfccb4d2510a925f32b1c558..6691054158037abdf698141d66b659abcdab2d37 100644
--- a/extraction/core/functions/loaders.py
+++ b/extraction/core/functions/loaders.py
@@ -1,4 +1,4 @@
-from inspect import getmembers, isfunction, getfullargspec
+from inspect import getfullargspec, getmembers, isfunction
 
 import numpy as np
 
diff --git a/extraction/examples/tiler_error.py b/extraction/examples/tiler_error.py
index aed61ae024a4a0f69b744d9e13dbb688cde34ae5..8997329619d1c61ebac2aaa91c4dca763b029118 100644
--- a/extraction/examples/tiler_error.py
+++ b/extraction/examples/tiler_error.py
@@ -1,6 +1,6 @@
+import matplotlib.pyplot as plt
 from core.experiment import Experiment
 from core.segment import Tiler
-import matplotlib.pyplot as plt
 
 expt = Experiment.from_source(
     19310,  # Experiment ID on OMERO
diff --git a/poetry.lock b/poetry.lock
index 676b5f7e37dd68d3145b22cbe649c2ca42626ff5..5414128d7cde4422067a068f7f98a71061de4a48 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -151,7 +151,7 @@ six = ">=1.6.1,<2.0"
 
 [[package]]
 name = "atomicwrites"
-version = "1.4.0"
+version = "1.4.1"
 description = "Atomic file writes."
 category = "dev"
 optional = false
@@ -271,6 +271,14 @@ python-versions = "*"
 [package.dependencies]
 pycparser = "*"
 
+[[package]]
+name = "cfgv"
+version = "3.3.1"
+description = "Validate configuration and produce human readable error messages."
+category = "dev"
+optional = false
+python-versions = ">=3.6.1"
+
 [[package]]
 name = "charset-normalizer"
 version = "2.1.0"
@@ -342,9 +350,20 @@ diagnostics = ["bokeh (>=2.1.1)", "jinja2"]
 distributed = ["distributed (==2021.12.0)"]
 test = ["pytest", "pytest-rerunfailures", "pytest-xdist", "pre-commit"]
 
+[[package]]
+name = "data-science-types"
+version = "0.2.23"
+description = "Type stubs for Python machine learning libraries"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+dev = ["black", "flake8", "flake8-pyi", "matplotlib", "mypy (==0.770)", "numpy", "pandas", "pytest"]
+
 [[package]]
 name = "debugpy"
-version = "1.6.0"
+version = "1.6.2"
 description = "An implementation of the Debug Adapter Protocol for Python"
 category = "dev"
 optional = false
@@ -379,7 +398,7 @@ graph = ["objgraph (>=1.7.2)"]
 
 [[package]]
 name = "distlib"
-version = "0.3.4"
+version = "0.3.5"
 description = "Distribution utilities"
 category = "main"
 optional = false
@@ -424,6 +443,20 @@ python-versions = ">=3.7"
 docs = ["furo (>=2021.8.17b43)", "sphinx (>=4.1)", "sphinx-autodoc-typehints (>=1.12)"]
 testing = ["covdefaults (>=1.2.0)", "coverage (>=4)", "pytest (>=4)", "pytest-cov", "pytest-timeout (>=1.4.2)"]
 
+[[package]]
+name = "flake8"
+version = "4.0.1"
+description = "the modular source code checker: pep8 pyflakes and co"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+importlib-metadata = {version = "<4.3", markers = "python_version < \"3.8\""}
+mccabe = ">=0.6.0,<0.7.0"
+pycodestyle = ">=2.8.0,<2.9.0"
+pyflakes = ">=2.4.0,<2.5.0"
+
 [[package]]
 name = "flatbuffers"
 version = "1.12"
@@ -434,7 +467,7 @@ python-versions = "*"
 
 [[package]]
 name = "fonttools"
-version = "4.33.3"
+version = "4.34.4"
 description = "Tools to manipulate font files"
 category = "main"
 optional = false
@@ -524,7 +557,7 @@ scipy = ">=1.7.3,<2.0.0"
 
 [[package]]
 name = "google-auth"
-version = "2.9.0"
+version = "2.9.1"
 description = "Google Authentication Library"
 category = "main"
 optional = false
@@ -594,6 +627,17 @@ python-versions = "*"
 numpy = ">=1.7"
 six = "*"
 
+[[package]]
+name = "identify"
+version = "2.5.1"
+description = "File identification library for Python"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+license = ["ukkonen"]
+
 [[package]]
 name = "idna"
 version = "3.3"
@@ -648,20 +692,19 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "4.12.0"
+version = "4.2.0"
 description = "Read metadata from Python packages"
 category = "main"
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.6"
 
 [package.dependencies]
 typing-extensions = {version = ">=3.6.4", markers = "python_version < \"3.8\""}
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-perf = ["ipython"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"]
+docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
+testing = ["pytest (>=4.6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
 
 [[package]]
 name = "importlib-resources"
@@ -688,7 +731,7 @@ python-versions = "*"
 
 [[package]]
 name = "ipykernel"
-version = "6.15.0"
+version = "6.15.1"
 description = "IPython Kernel for Jupyter"
 category = "dev"
 optional = false
@@ -822,7 +865,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "jsonschema"
-version = "4.6.1"
+version = "4.7.2"
 description = "An implementation of JSON Schema validation for Python"
 category = "main"
 optional = false
@@ -896,7 +939,7 @@ test = ["pexpect"]
 
 [[package]]
 name = "jupyter-core"
-version = "4.10.0"
+version = "4.11.1"
 description = "Jupyter core package. A base package on which Jupyter projects rely."
 category = "dev"
 optional = false
@@ -1012,15 +1055,12 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "markdown"
-version = "3.3.7"
+version = "3.3.5"
 description = "Python implementation of Markdown."
 category = "main"
 optional = false
 python-versions = ">=3.6"
 
-[package.dependencies]
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
-
 [package.extras]
 testing = ["coverage", "pyyaml"]
 
@@ -1062,6 +1102,14 @@ python-versions = ">=3.5"
 [package.dependencies]
 traitlets = "*"
 
+[[package]]
+name = "mccabe"
+version = "0.6.1"
+description = "McCabe checker, plugin for flake8"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "mistune"
 version = "0.8.4"
@@ -1214,6 +1262,14 @@ doc = ["sphinx (>=4.0,<5.0)", "pydata-sphinx-theme (>=0.6,<1.0)", "sphinx-galler
 extra = ["lxml (>=4.5)", "pygraphviz (>=1.7)", "pydot (>=1.4.1)"]
 test = ["pytest (>=6.2)", "pytest-cov (>=2.12)", "codecov (>=2.1)"]
 
+[[package]]
+name = "nodeenv"
+version = "1.7.0"
+description = "Node.js virtual environment builder"
+category = "dev"
+optional = false
+python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
+
 [[package]]
 name = "notebook"
 version = "6.4.12"
@@ -1506,6 +1562,23 @@ six = ">=1.7.3"
 [package.extras]
 dill = ["dill (>=0.3.5)"]
 
+[[package]]
+name = "pre-commit"
+version = "2.20.0"
+description = "A framework for managing and maintaining multi-language pre-commit hooks."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+cfgv = ">=2.0.0"
+identify = ">=1.0.0"
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
+nodeenv = ">=0.11.1"
+pyyaml = ">=5.1"
+toml = "*"
+virtualenv = ">=20.0.8"
+
 [[package]]
 name = "prometheus-client"
 version = "0.14.1"
@@ -1601,6 +1674,14 @@ category = "main"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "pycodestyle"
+version = "2.8.0"
+description = "Python style guide checker"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "pycparser"
 version = "2.21"
@@ -1636,6 +1717,22 @@ python-versions = ">=3.6.8"
 [package.extras]
 diagrams = ["railroad-diagrams", "jinja2"]
 
+[[package]]
+name = "pyright"
+version = "1.1.260"
+description = "Command line wrapper for pyright"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.dependencies]
+nodeenv = ">=1.6.0"
+typing-extensions = {version = ">=3.7", markers = "python_version < \"3.8\""}
+
+[package.extras]
+all = ["twine (>=3.4.1)"]
+dev = ["twine (>=3.4.1)"]
+
 [[package]]
 name = "pyrsistent"
 version = "0.18.1"
@@ -1706,7 +1803,7 @@ python-versions = "*"
 
 [[package]]
 name = "pywinpty"
-version = "2.0.5"
+version = "2.0.6"
 description = "Pseudo terminal support for Windows from Python."
 category = "dev"
 optional = false
@@ -1943,7 +2040,7 @@ win32 = ["pywin32"]
 
 [[package]]
 name = "setuptools-scm"
-version = "7.0.4"
+version = "7.0.5"
 description = "the blessed package to manage your versions by scm tags"
 category = "main"
 optional = false
@@ -1985,7 +2082,7 @@ python-versions = ">=3.6"
 
 [[package]]
 name = "sphinx"
-version = "4.5.0"
+version = "4.3.2"
 description = "Python documentation generator"
 category = "dev"
 optional = false
@@ -1997,7 +2094,6 @@ babel = ">=1.3"
 colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
 docutils = ">=0.14,<0.18"
 imagesize = "*"
-importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""}
 Jinja2 = ">=2.3"
 packaging = "*"
 Pygments = ">=2.0"
@@ -2012,7 +2108,7 @@ sphinxcontrib-serializinghtml = ">=1.1.5"
 
 [package.extras]
 docs = ["sphinxcontrib-websupport"]
-lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.931)", "docutils-stubs", "types-typed-ast", "types-requests"]
+lint = ["flake8 (>=3.5.0)", "isort", "mypy (>=0.920)", "docutils-stubs", "types-typed-ast", "types-pkg-resources", "types-requests"]
 test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
 
 [[package]]
@@ -2287,7 +2383,7 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "toolz"
-version = "0.11.2"
+version = "0.12.0"
 description = "List processing tools and functional utilities"
 category = "main"
 optional = false
@@ -2295,11 +2391,11 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "tornado"
-version = "6.1"
+version = "6.2"
 description = "Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed."
 category = "dev"
 optional = false
-python-versions = ">= 3.5"
+python-versions = ">= 3.7"
 
 [[package]]
 name = "tqdm"
@@ -2361,11 +2457,11 @@ python-versions = ">=3.7"
 
 [[package]]
 name = "urllib3"
-version = "1.26.9"
+version = "1.26.10"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 category = "main"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4"
 
 [package.extras]
 brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
@@ -2474,20 +2570,20 @@ python-versions = "*"
 
 [[package]]
 name = "zipp"
-version = "3.8.0"
+version = "3.8.1"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 category = "main"
 optional = false
 python-versions = ">=3.7"
 
 [package.extras]
-docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
+docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)", "jaraco.tidelift (>=1.4)"]
+testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "jaraco.itertools", "func-timeout", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)"]
 
 [metadata]
 lock-version = "1.1"
 python-versions = ">=3.7.1,<3.11"
-content-hash = "ca727c3f62b8f830b216b8c7066fe03174c90ab905aa8d371b9f34e112499468"
+content-hash = "822f4d47d564f2a618ca9d978de9abd442e4770905f2865de2edb917f8b47674"
 
 [metadata.files]
 absl-py = [
@@ -2550,10 +2646,7 @@ astunparse = [
     {file = "astunparse-1.6.3-py2.py3-none-any.whl", hash = "sha256:c2652417f2c8b5bb325c885ae329bdf3f86424075c4fd1a128674bc6fba4b8e8"},
     {file = "astunparse-1.6.3.tar.gz", hash = "sha256:5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872"},
 ]
-atomicwrites = [
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@@ -3695,6 +3752,7 @@ pyasn1-modules = [
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@@ -3711,6 +3769,7 @@ pyparsing = [
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     {file = "pyparsing-3.0.9.tar.gz", hash = "sha256:2b020ecf7d21b687f219b71ecad3631f644a47f01403fa1d1036b0c6416d70fb"},
 ]
+pyright = []
 pyrsistent = [
     {file = "pyrsistent-0.18.1-cp310-cp310-macosx_10_9_universal2.whl", hash = "sha256:df46c854f490f81210870e509818b729db4488e1f30f2a1ce1698b2295a878d1"},
     {file = "pyrsistent-0.18.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl", hash = "sha256:5d45866ececf4a5fff8742c25722da6d4c9e180daa7b405dc0a2a2790d668c26"},
@@ -3794,13 +3853,7 @@ pywin32 = [
     {file = "pywin32-304-cp39-cp39-win32.whl", hash = "sha256:25746d841201fd9f96b648a248f731c1dec851c9a08b8e33da8b56148e4c65cc"},
     {file = "pywin32-304-cp39-cp39-win_amd64.whl", hash = "sha256:d24a3382f013b21aa24a5cfbfad5a2cd9926610c0affde3e8ab5b3d7dbcf4ac9"},
 ]
-pywinpty = [
-    {file = "pywinpty-2.0.5-cp310-none-win_amd64.whl", hash = "sha256:f86c76e2881c37e69678cbbf178109f8da1fa8584db24d58e1b9369b0276cfcb"},
-    {file = "pywinpty-2.0.5-cp37-none-win_amd64.whl", hash = "sha256:ff9b52f182650cfdf3db1b264a6fe0963eb9d996a7a1fa843ac406c1e32111f8"},
-    {file = "pywinpty-2.0.5-cp38-none-win_amd64.whl", hash = "sha256:651ee1467bd7eb6f64d44dbc954b7ab7d15ab6d8adacc4e13299692c67c5d5d2"},
-    {file = "pywinpty-2.0.5-cp39-none-win_amd64.whl", hash = "sha256:e59a508ae78374febada3e53b5bbc90b5ad07ae68cbfd72a2e965f9793ae04f3"},
-    {file = "pywinpty-2.0.5.tar.gz", hash = "sha256:e125d3f1804d8804952b13e33604ad2ca8b9b2cac92b27b521c005d1604794f8"},
-]
+pywinpty = []
 pyyaml = [
     {file = "PyYAML-6.0-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:d4db7c7aef085872ef65a8fd7d6d09a14ae91f691dec3e87ee5ee0539d516f53"},
     {file = "PyYAML-6.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:9df7ed3b3d2e0ecfe09e14741b857df43adb5a3ddadc919a2d94fbdf78fea53c"},
@@ -4024,10 +4077,7 @@ send2trash = [
     {file = "Send2Trash-1.8.0-py3-none-any.whl", hash = "sha256:f20eaadfdb517eaca5ce077640cb261c7d2698385a6a0f072a4a5447fd49fa08"},
     {file = "Send2Trash-1.8.0.tar.gz", hash = "sha256:d2c24762fd3759860a0aff155e45871447ea58d2be6bdd39b5c8f966a0c99c2d"},
 ]
-setuptools-scm = [
-    {file = "setuptools_scm-7.0.4-py3-none-any.whl", hash = "sha256:53a6f51451a84d891ca485cec700a802413bbc5e76ee65da134e54c733a6e44d"},
-    {file = "setuptools_scm-7.0.4.tar.gz", hash = "sha256:c27bc1f48593cfc9527251f1f0fc41ce282ea57bbc7fd5a1ea3acb99325fab4c"},
-]
+setuptools-scm = []
 six = [
     {file = "six-1.16.0-py2.py3-none-any.whl", hash = "sha256:8abb2f1d86890a2dfb989f9a77cfcfd3e47c2a354b01111771326f8aa26e0254"},
     {file = "six-1.16.0.tar.gz", hash = "sha256:1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926"},
@@ -4040,10 +4090,7 @@ soupsieve = [
     {file = "soupsieve-2.3.2.post1-py3-none-any.whl", hash = "sha256:3b2503d3c7084a42b1ebd08116e5f81aadfaea95863628c80a3b774a11b7c759"},
     {file = "soupsieve-2.3.2.post1.tar.gz", hash = "sha256:fc53893b3da2c33de295667a0e19f078c14bf86544af307354de5fcf12a3f30d"},
 ]
-sphinx = [
-    {file = "Sphinx-4.5.0-py3-none-any.whl", hash = "sha256:ebf612653238bcc8f4359627a9b7ce44ede6fdd75d9d30f68255c7383d3a6226"},
-    {file = "Sphinx-4.5.0.tar.gz", hash = "sha256:7bf8ca9637a4ee15af412d1a1d9689fec70523a68ca9bb9127c2f3eeb344e2e6"},
-]
+sphinx = []
 sphinxcontrib-applehelp = [
     {file = "sphinxcontrib-applehelp-1.0.2.tar.gz", hash = "sha256:a072735ec80e7675e3f432fcae8610ecf509c5f1869d17e2eecff44389cdbc58"},
     {file = "sphinxcontrib_applehelp-1.0.2-py2.py3-none-any.whl", hash = "sha256:806111e5e962be97c29ec4c1e7fe277bfd19e9652fb1a4392105b43e01af885a"},
@@ -4154,53 +4201,8 @@ tomli = [
     {file = "tomli-2.0.1-py3-none-any.whl", hash = "sha256:939de3e7a6161af0c887ef91b7d41a53e7c5a1ca976325f429cb46ea9bc30ecc"},
     {file = "tomli-2.0.1.tar.gz", hash = "sha256:de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f"},
 ]
-toolz = [
-    {file = "toolz-0.11.2-py3-none-any.whl", hash = "sha256:a5700ce83414c64514d82d60bcda8aabfde092d1c1a8663f9200c07fdcc6da8f"},
-    {file = "toolz-0.11.2.tar.gz", hash = "sha256:6b312d5e15138552f1bda8a4e66c30e236c831b612b2bf0005f8a1df10a4bc33"},
-]
-tornado = [
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-    {file = "tornado-6.1-cp35-cp35m-manylinux1_i686.whl", hash = "sha256:0d321a39c36e5f2c4ff12b4ed58d41390460f798422c4504e09eb5678e09998c"},
-    {file = "tornado-6.1-cp35-cp35m-manylinux1_x86_64.whl", hash = "sha256:9de9e5188a782be6b1ce866e8a51bc76a0fbaa0e16613823fc38e4fc2556ad05"},
-    {file = "tornado-6.1-cp35-cp35m-manylinux2010_i686.whl", hash = "sha256:61b32d06ae8a036a6607805e6720ef00a3c98207038444ba7fd3d169cd998910"},
-    {file = "tornado-6.1-cp35-cp35m-manylinux2010_x86_64.whl", hash = "sha256:3e63498f680547ed24d2c71e6497f24bca791aca2fe116dbc2bd0ac7f191691b"},
-    {file = "tornado-6.1-cp35-cp35m-manylinux2014_aarch64.whl", hash = "sha256:6c77c9937962577a6a76917845d06af6ab9197702a42e1346d8ae2e76b5e3675"},
-    {file = "tornado-6.1-cp35-cp35m-win32.whl", hash = "sha256:6286efab1ed6e74b7028327365cf7346b1d777d63ab30e21a0f4d5b275fc17d5"},
-    {file = "tornado-6.1-cp35-cp35m-win_amd64.whl", hash = "sha256:fa2ba70284fa42c2a5ecb35e322e68823288a4251f9ba9cc77be04ae15eada68"},
-    {file = "tornado-6.1-cp36-cp36m-macosx_10_9_x86_64.whl", hash = "sha256:0a00ff4561e2929a2c37ce706cb8233b7907e0cdc22eab98888aca5dd3775feb"},
-    {file = "tornado-6.1-cp36-cp36m-manylinux1_i686.whl", hash = "sha256:748290bf9112b581c525e6e6d3820621ff020ed95af6f17fedef416b27ed564c"},
-    {file = "tornado-6.1-cp36-cp36m-manylinux1_x86_64.whl", hash = "sha256:e385b637ac3acaae8022e7e47dfa7b83d3620e432e3ecb9a3f7f58f150e50921"},
-    {file = "tornado-6.1-cp36-cp36m-manylinux2010_i686.whl", hash = "sha256:25ad220258349a12ae87ede08a7b04aca51237721f63b1808d39bdb4b2164558"},
-    {file = "tornado-6.1-cp36-cp36m-manylinux2010_x86_64.whl", hash = "sha256:65d98939f1a2e74b58839f8c4dab3b6b3c1ce84972ae712be02845e65391ac7c"},
-    {file = "tornado-6.1-cp36-cp36m-manylinux2014_aarch64.whl", hash = "sha256:e519d64089b0876c7b467274468709dadf11e41d65f63bba207e04217f47c085"},
-    {file = "tornado-6.1-cp36-cp36m-win32.whl", hash = "sha256:b87936fd2c317b6ee08a5741ea06b9d11a6074ef4cc42e031bc6403f82a32575"},
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-    {file = "tornado-6.1-cp37-cp37m-win32.whl", hash = "sha256:e7229e60ac41a1202444497ddde70a48d33909e484f96eb0da9baf8dc68541df"},
-    {file = "tornado-6.1-cp37-cp37m-win_amd64.whl", hash = "sha256:cb5ec8eead331e3bb4ce8066cf06d2dfef1bfb1b2a73082dfe8a161301b76e37"},
-    {file = "tornado-6.1-cp38-cp38-macosx_10_9_x86_64.whl", hash = "sha256:20241b3cb4f425e971cb0a8e4ffc9b0a861530ae3c52f2b0434e6c1b57e9fd95"},
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-    {file = "tornado-6.1-cp38-cp38-manylinux1_x86_64.whl", hash = "sha256:fba85b6cd9c39be262fcd23865652920832b61583de2a2ca907dbd8e8a8c81e5"},
-    {file = "tornado-6.1-cp38-cp38-manylinux2010_i686.whl", hash = "sha256:1e8225a1070cd8eec59a996c43229fe8f95689cb16e552d130b9793cb570a288"},
-    {file = "tornado-6.1-cp38-cp38-manylinux2010_x86_64.whl", hash = "sha256:d14d30e7f46a0476efb0deb5b61343b1526f73ebb5ed84f23dc794bdb88f9d9f"},
-    {file = "tornado-6.1-cp38-cp38-manylinux2014_aarch64.whl", hash = "sha256:8f959b26f2634a091bb42241c3ed8d3cedb506e7c27b8dd5c7b9f745318ddbb6"},
-    {file = "tornado-6.1-cp38-cp38-win32.whl", hash = "sha256:34ca2dac9e4d7afb0bed4677512e36a52f09caa6fded70b4e3e1c89dbd92c326"},
-    {file = "tornado-6.1-cp38-cp38-win_amd64.whl", hash = "sha256:6196a5c39286cc37c024cd78834fb9345e464525d8991c21e908cc046d1cc02c"},
-    {file = "tornado-6.1-cp39-cp39-macosx_10_9_x86_64.whl", hash = "sha256:f0ba29bafd8e7e22920567ce0d232c26d4d47c8b5cf4ed7b562b5db39fa199c5"},
-    {file = "tornado-6.1-cp39-cp39-manylinux1_i686.whl", hash = "sha256:33892118b165401f291070100d6d09359ca74addda679b60390b09f8ef325ffe"},
-    {file = "tornado-6.1-cp39-cp39-manylinux1_x86_64.whl", hash = "sha256:7da13da6f985aab7f6f28debab00c67ff9cbacd588e8477034c0652ac141feea"},
-    {file = "tornado-6.1-cp39-cp39-manylinux2010_i686.whl", hash = "sha256:e0791ac58d91ac58f694d8d2957884df8e4e2f6687cdf367ef7eb7497f79eaa2"},
-    {file = "tornado-6.1-cp39-cp39-manylinux2010_x86_64.whl", hash = "sha256:66324e4e1beede9ac79e60f88de548da58b1f8ab4b2f1354d8375774f997e6c0"},
-    {file = "tornado-6.1-cp39-cp39-manylinux2014_aarch64.whl", hash = "sha256:a48900ecea1cbb71b8c71c620dee15b62f85f7c14189bdeee54966fbd9a0c5bd"},
-    {file = "tornado-6.1-cp39-cp39-win32.whl", hash = "sha256:d3d20ea5782ba63ed13bc2b8c291a053c8d807a8fa927d941bd718468f7b950c"},
-    {file = "tornado-6.1-cp39-cp39-win_amd64.whl", hash = "sha256:548430be2740e327b3fe0201abe471f314741efcb0067ec4f2d7dcfb4825f3e4"},
-    {file = "tornado-6.1.tar.gz", hash = "sha256:33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791"},
-]
+toolz = []
+tornado = []
 tqdm = [
     {file = "tqdm-4.64.0-py2.py3-none-any.whl", hash = "sha256:74a2cdefe14d11442cedf3ba4e21a3b84ff9a2dbdc6cfae2c34addb2a14a5ea6"},
     {file = "tqdm-4.64.0.tar.gz", hash = "sha256:40be55d30e200777a307a7585aee69e4eabb46b4ec6a4b4a5f2d9f11e7d5408d"},
@@ -4242,10 +4244,7 @@ typing-extensions = [
     {file = "typing_extensions-4.3.0-py3-none-any.whl", hash = "sha256:25642c956049920a5aa49edcdd6ab1e06d7e5d467fc00e0506c44ac86fbfca02"},
     {file = "typing_extensions-4.3.0.tar.gz", hash = "sha256:e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6"},
 ]
-urllib3 = [
-    {file = "urllib3-1.26.9-py2.py3-none-any.whl", hash = "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14"},
-    {file = "urllib3-1.26.9.tar.gz", hash = "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"},
-]
+urllib3 = []
 virtualenv = [
     {file = "virtualenv-20.15.1-py2.py3-none-any.whl", hash = "sha256:b30aefac647e86af6d82bfc944c556f8f1a9c90427b2fb4e3bfbf338cb82becf"},
     {file = "virtualenv-20.15.1.tar.gz", hash = "sha256:288171134a2ff3bfb1a2f54f119e77cd1b81c29fc1265a2356f3e8d14c7d58c4"},
@@ -4352,7 +4351,4 @@ zeroc-ice = [
     {file = "zeroc_ice-3.6.5-cp37-cp37m-win32.whl", hash = "sha256:b9d9e00e2ee649971e3615752531d73577daedbc8a0ac04178727651f1ed4fa2"},
     {file = "zeroc_ice-3.6.5-cp37-cp37m-win_amd64.whl", hash = "sha256:cdc4c68111dfe3542287ca6d41d2ad7ee22d8806cf6231f124769c60351d636c"},
 ]
-zipp = [
-    {file = "zipp-3.8.0-py3-none-any.whl", hash = "sha256:c4f6e5bbf48e74f7a38e7cc5b0480ff42b0ae5178957d564d18932525d5cf099"},
-    {file = "zipp-3.8.0.tar.gz", hash = "sha256:56bf8aadb83c24db6c4b577e13de374ccfb67da2078beba1d037c17980bf43ad"},
-]
+zipp = []
diff --git a/pyproject.toml b/pyproject.toml
index ab210eb2691f455ffde7fa67b4a38896bfb5302f..abaaa79bca85d9c4e851fbde9aa989a01b0b27ac 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "aliby"
-version = "0.1.35"
+version = "0.1.36"
 description = "Process and analyse live-cell imaging data"
 authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
 packages = [
@@ -32,16 +32,18 @@ xmltodict = "^0.13.0" # read ome-tiff metadata
 zeroc-ice = {version="3.6.5"} # networking interface, slow to build
 # zeroc-ice = {version="3.6.5", optional=true} # To be set as optional in the future
 
-
 [tool.poetry.dev-dependencies]
-black = "^22.3.0"
+black = "^22.6.0"
 Sphinx = "^4.3.2"
 pytest = "^6.2.5"
 mypy = "^0.930"
 numpydoc = "^1.3.1"
-pyflakes = "^2.4.0"
 isort = "^5.10.1"
 jupyter = "^1.0.0"
+flake8 = "^4.0.1"
+pyright = "^1.1.258"
+pre-commit = "^2.20.0"
+data-science-types = "^0.2.23"
 
 [build-system]
 requires = ["setuptools", "poetry-core>=1.0.0"]
@@ -52,12 +54,21 @@ line-length = 79
 target-version = ['py37']
 include = '\.pyi?$'
 extend-exclude = '''
-# A regex preceded with ^/ will apply only to files and directories
-# in the root of the project.
-^/foo.py  # exclude a file named foo.py in the root of the project (in addition to the defaults)
+/(
+    \.git
+  | \.hg
+  | \.mypy_cache
+  | \.tox
+  | \.venv
+  | _build
+  | buck-out
+  | build
+  | dist
+)/
 '''
+
 [tool.isort]
+profile = "black"
 multi_line_output = 3
 line_length = 79
 include_trailing_comma = true
-
diff --git a/setup.py b/setup.py
index 965bbc5d20ebce102fa6744c42b2f49a27dca453..d8ed940170488783738b2e6ff7a6d71b05ecda90 100644
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,4 @@
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 print("find_packages outputs ", find_packages("aliby"))
 setup(
diff --git a/tests/aliby/connect_to_omero.py b/tests/alib/test_connect_to_omero.py
similarity index 100%
rename from tests/aliby/connect_to_omero.py
rename to tests/alib/test_connect_to_omero.py
diff --git a/tests/aliby/test_post_processing.py b/tests/aliby/test_post_processing.py
index 8dc68ae45bb6355513b1a03825a40767035ae413..3ac8ba403602778a92fa482f4c64395df59663b0 100644
--- a/tests/aliby/test_post_processing.py
+++ b/tests/aliby/test_post_processing.py
@@ -1,8 +1,8 @@
-import pytest
 import unittest
 
 import matplotlib.pyplot as plt
 import numpy as np
+import pytest
 import skimage.morphology as morph
 from scipy import ndimage
 from skimage import draw
diff --git a/tests/extraction/log_test.py b/tests/extraction/test_log.py
similarity index 100%
rename from tests/extraction/log_test.py
rename to tests/extraction/test_log.py