From 4b58bf649138eabc417f15d0e7df134ec5b893fd Mon Sep 17 00:00:00 2001
From: Anton Rau <anton.rau@gmail.com>
Date: Fri, 21 May 2021 14:27:00 +0200
Subject: [PATCH] - Fix: broken assertion (#110). - Fix: ome2histocat stripps
 .tiff file ending from masks (#111).

---
 .github/workflows/docs.yml                 |   2 +-
 .github/workflows/test_and_deploy.yml      |   4 +-
 CHANGELOG.md                               |   4 +
 docs/source/quickstart.md                  |   2 +-
 imctools/__init__.py                       |   2 +-
 imctools/converters/mcdfolder2imcfolder.py |   4 +-
 imctools/converters/ome2analysis.py        |  16 +-
 imctools/converters/ome2histocat.py        |   7 +-
 poetry.lock                                | 636 ++++++++++-----------
 pyproject.toml                             |   4 +-
 10 files changed, 315 insertions(+), 366 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index cc04860..644b6d3 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -23,7 +23,7 @@ jobs:
         with:
           docs-folder: docs/
           build-command: make html
-          pre-build-command: python -m pip install --upgrade pip && pip install poetry==1.1.5 && poetry config virtualenvs.create false && poetry install
+          pre-build-command: python -m pip install --upgrade pip && pip install poetry==1.1.6 && poetry config virtualenvs.create false && poetry install
       - name: Commit documentation changes
         run: |
           cp -r docs/build/html/* gh-pages/
diff --git a/.github/workflows/test_and_deploy.yml b/.github/workflows/test_and_deploy.yml
index 8b56eec..a7b2191 100644
--- a/.github/workflows/test_and_deploy.yml
+++ b/.github/workflows/test_and_deploy.yml
@@ -31,7 +31,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install poetry==1.1.5
+          pip install poetry==1.1.6
           poetry install
         env:
           POETRY_VIRTUALENVS_CREATE: false
@@ -55,7 +55,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install poetry==1.1.5
+          pip install poetry==1.1.6
           poetry install --no-dev
         env:
           POETRY_VIRTUALENVS_CREATE: false
diff --git a/CHANGELOG.md b/CHANGELOG.md
index b439529..65b5b4e 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [2.1.7] - 2021-05-21
+- Fix: broken assertion (#110).
+- Fix: ome2histocat stripps .tiff file ending from masks (#111).
+
 ## [2.1.6] - 2021-03-16
 - Allows `mcdfolder_to_imcfolder` to convert data from sub-folders in zip file.
 
diff --git a/docs/source/quickstart.md b/docs/source/quickstart.md
index 6559540..bcbf506 100644
--- a/docs/source/quickstart.md
+++ b/docs/source/quickstart.md
@@ -29,7 +29,7 @@ Version 1.x documentation (deprecated): https://imctools.readthedocs.io
 
 Preferable way to install `imctools` is via official PyPI registry. Please define package version explicitly in order to avoid incompatibilities between v1.x and v2.x versions:
 ```
-pip install imctools==2.1.4
+pip install imctools==2.1.7
 ```
 In old IMC segmentation pipelines versions 1.x should be used!
 ```
diff --git a/imctools/__init__.py b/imctools/__init__.py
index d037d75..f4e6d2a 100644
--- a/imctools/__init__.py
+++ b/imctools/__init__.py
@@ -6,4 +6,4 @@
 
 __author__ = """Vito Zanotelli, Anton Rau"""
 __email__ = "vito.zanotelli@uzh.ch, anton.rau@uzh.ch"
-__version__ = "2.1.6"
+__version__ = "2.1.7"
diff --git a/imctools/converters/mcdfolder2imcfolder.py b/imctools/converters/mcdfolder2imcfolder.py
index 3f7f737..907b38b 100644
--- a/imctools/converters/mcdfolder2imcfolder.py
+++ b/imctools/converters/mcdfolder2imcfolder.py
@@ -75,10 +75,10 @@ def mcdfolder_to_imcfolder(
     tic = timeit.default_timer()
 
     mcdfolder_to_imcfolder(
-        # Path("/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa.zip"),
+        Path("/home/anton/Data/ImcSegmentationPipelineV2/20191202_HuBMAP_LympNode_ED.zip"),
         # "/home/anton/Downloads/20170905_Fluidigmworkshopfinal_SEAJa",
         # "/home/anton/Data/forAnton_MCD/6505_Lympho",
-        "/home/anton/Downloads/IMMUcan_Batch20201113_10042702-GU-VAR-TIS-01-IMC-01.zip",
+        # "/home/anton/Downloads/IMMUcan_Batch20201113_10042702-GU-VAR-TIS-01-IMC-01.zip",
         # "/home/anton/Documents/merrick/IMC/20200904_MS_XRF_epithelial_panel_4_titration.zip",
         # "/home/anton/Documents/IMC Workshop 2019/Data/iMC_workshop_2019/20190919_FluidigmBrCa_SE",
         # "/home/anton/Downloads/test",
diff --git a/imctools/converters/ome2analysis.py b/imctools/converters/ome2analysis.py
index 8b280ab..e4c1bcb 100644
--- a/imctools/converters/ome2analysis.py
+++ b/imctools/converters/ome2analysis.py
@@ -34,13 +34,13 @@ def get_metals_from_panel(
 
     if panel_csv_file is not None:
 
-        pannel = pd.read_csv(panel_csv_file)
-        if pannel.shape[1] > 1:
-            selected = pannel[usedcolumn]
-            assert selected.any() == 0 or selected.any() == 1, f"Values in 'usedcolumn' column should contain only 0/1"
-            metals = [str(n) for s, n in zip(selected, pannel[metalcolumn]) if s]
+        panel = pd.read_csv(panel_csv_file)
+        if panel.shape[1] > 1:
+            selected = panel[usedcolumn]
+            assert selected.isin((0, 1)).all(), f"Values in 'usedcolumn' column should contain only 0/1"
+            metals = panel.loc[selected == 1, metalcolumn].tolist()
         else:
-            metals = [pannel.columns[0]] + pannel.iloc[:, 0].tolist()
+            metals = [panel.columns[0]] + panel.iloc[:, 0].tolist()
 
     if sort_channels:
         if metals is not None:
@@ -187,9 +187,9 @@ def omefolder_to_analysisfolder(
     # )
 
     omefolder_to_analysisfolder(
-        "/home/anton/Downloads/imc_folder",
+        "/home/anton/Downloads/imc_folder_v2",
         "/home/anton/Downloads/analysis_folder",
-        "/home/anton/Downloads/example_panel.csv",
+        "/home/anton/Data/ImcSegmentationPipelineV2/hubmap_processed_v2/panel.csv",
         [("ilastik", "_ilastik", True), ("full", "_full", False)],
         metalcolumn="Metal Tag",
     )
diff --git a/imctools/converters/ome2histocat.py b/imctools/converters/ome2histocat.py
index de9b8c3..bf7f14b 100644
--- a/imctools/converters/ome2histocat.py
+++ b/imctools/converters/ome2histocat.py
@@ -68,9 +68,7 @@ def omefile_to_histocatfolder(
     if mask_file is not None:
         if isinstance(mask_file, str):
             mask_file = Path(mask_file)
-        fn_mask_base = mask_file.stem
-        fn_mask_new = output_folder / fn_mask_base
-        shutil.copy2(mask_file, fn_mask_new)
+        shutil.copy2(mask_file, output_folder)
 
 
 def omefolder_to_histocatfolder(
@@ -127,8 +125,9 @@ def omefolder_to_histocatfolder(
     tic = timeit.default_timer()
 
     omefolder_to_histocatfolder(
-        Path("/home/anton/Downloads/imc_folder/20170905_Fluidigmworkshopfinal_SEAJa"),
+        Path("/home/anton/Downloads/imc_folder_v2/20191203_HuBMAP_LN"),
         Path("/home/anton/Downloads/tiff_folder"),
+        mask_folder="/home/anton/Data/ImcSegmentationPipelineV2/hubmap_processed_v2/masks",
     )
 
     print(timeit.default_timer() - tic)
diff --git a/poetry.lock b/poetry.lock
index 78122f9..ea170e8 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -16,11 +16,11 @@ python-versions = "*"
 
 [[package]]
 name = "astroid"
-version = "2.5.1"
+version = "2.5.6"
 description = "An abstract syntax tree for Python with inference support."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = "~=3.6"
 
 [package.dependencies]
 lazy-object-proxy = ">=1.4.0"
@@ -37,17 +37,17 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "attrs"
-version = "20.3.0"
+version = "19.3.0"
 description = "Classes Without Boilerplate"
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [package.extras]
-dev = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "furo", "sphinx", "pre-commit"]
-docs = ["furo", "sphinx", "zope.interface"]
-tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
-tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (>=4.3.0)", "six"]
+azure-pipelines = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "pytest-azurepipelines"]
+dev = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface", "sphinx", "pre-commit"]
+docs = ["sphinx", "zope.interface"]
+tests = ["coverage", "hypothesis", "pympler", "pytest (>=4.3.0)", "six", "zope.interface"]
 
 [[package]]
 name = "autoflake"
@@ -62,7 +62,7 @@ pyflakes = ">=1.1.0"
 
 [[package]]
 name = "babel"
-version = "2.9.0"
+version = "2.9.1"
 description = "Internationalization utilities"
 category = "dev"
 optional = false
@@ -73,25 +73,26 @@ pytz = ">=2015.7"
 
 [[package]]
 name = "black"
-version = "20.8b1"
+version = "21.5b1"
 description = "The uncompromising code formatter."
 category = "dev"
 optional = false
-python-versions = ">=3.6"
+python-versions = ">=3.6.2"
 
 [package.dependencies]
 appdirs = "*"
 click = ">=7.1.2"
 mypy-extensions = ">=0.4.3"
-pathspec = ">=0.6,<1"
+pathspec = ">=0.8.1,<1"
 regex = ">=2020.1.8"
 toml = ">=0.10.1"
-typed-ast = ">=1.4.0"
-typing-extensions = ">=3.7.4"
+typed-ast = {version = ">=1.4.2", markers = "python_version < \"3.8\""}
+typing-extensions = {version = ">=3.7.4", markers = "python_version < \"3.8\""}
 
 [package.extras]
 colorama = ["colorama (>=0.4.3)"]
-d = ["aiohttp (>=3.3.2)", "aiohttp-cors"]
+d = ["aiohttp (>=3.6.0)", "aiohttp-cors"]
+python2 = ["typed-ast (>=1.4.2)"]
 
 [[package]]
 name = "certifi"
@@ -111,11 +112,15 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "click"
-version = "7.1.2"
+version = "8.0.1"
 description = "Composable command line interface toolkit"
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
+
+[package.dependencies]
+colorama = {version = "*", markers = "platform_system == \"Windows\""}
+importlib-metadata = {version = "*", markers = "python_version < \"3.8\""}
 
 [[package]]
 name = "colorama"
@@ -133,6 +138,9 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4"
 
+[package.dependencies]
+toml = {version = "*", optional = true, markers = "extra == \"toml\""}
+
 [package.extras]
 toml = ["toml"]
 
@@ -146,7 +154,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [[package]]
 name = "flake8"
-version = "3.9.0"
+version = "3.9.2"
 description = "the modular source code checker: pep8 pyflakes and co"
 category = "dev"
 optional = false
@@ -168,7 +176,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "imagecodecs"
-version = "2021.2.26"
+version = "2021.4.28"
 description = "Image transformation, compression, and decompression codecs"
 category = "main"
 optional = false
@@ -178,7 +186,7 @@ python-versions = ">=3.7"
 numpy = ">=1.15.1"
 
 [package.extras]
-all = ["matplotlib (>=3.2)", "tifffile (>=2021.1.11)"]
+all = ["matplotlib (>=3.2)", "tifffile (>=2021.1.11)", "numcodecs"]
 
 [[package]]
 name = "imagesize"
@@ -190,7 +198,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "importlib-metadata"
-version = "3.7.3"
+version = "4.0.1"
 description = "Read metadata from Python packages"
 category = "dev"
 optional = false
@@ -202,7 +210,7 @@ zipp = ">=0.5"
 
 [package.extras]
 docs = ["sphinx", "jaraco.packaging (>=8.2)", "rst.linker (>=1.9)"]
-testing = ["pytest (>=3.5,!=3.7.3)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pytest-cov", "pytest-enabler", "packaging", "pep517", "pyfakefs", "flufl.flake8", "pytest-black (>=0.3.7)", "pytest-mypy", "importlib-resources (>=1.3)"]
+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 = "iniconfig"
@@ -214,7 +222,7 @@ python-versions = "*"
 
 [[package]]
 name = "isort"
-version = "5.7.0"
+version = "5.8.0"
 description = "A Python utility / library to sort Python imports."
 category = "dev"
 optional = false
@@ -227,52 +235,50 @@ colors = ["colorama (>=0.4.3,<0.5.0)"]
 
 [[package]]
 name = "jinja2"
-version = "2.11.3"
+version = "3.0.1"
 description = "A very fast and expressive template engine."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=3.6"
 
 [package.dependencies]
-MarkupSafe = ">=0.23"
+MarkupSafe = ">=2.0"
 
 [package.extras]
-i18n = ["Babel (>=0.8)"]
+i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "lazy-object-proxy"
-version = "1.5.2"
+version = "1.6.0"
 description = "A fast and thorough lazy object proxy."
 category = "dev"
 optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
 
 [[package]]
 name = "markdown-it-py"
-version = "0.6.2"
+version = "0.4.9"
 description = "Python port of markdown-it. Markdown parsing, done right!"
 category = "dev"
 optional = false
 python-versions = "~=3.6"
 
 [package.dependencies]
-attrs = ">=19,<21"
-mdit-py-plugins = ">=0.2.1,<0.3.0"
+attrs = ">=19.3,<20.0"
 
 [package.extras]
-code_style = ["pre-commit (==2.6)"]
-compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.2.2,<3.3.0)", "mistune (>=0.8.4,<0.9.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "panflute (>=1.12,<2.0)"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
-rtd = ["myst-nb (>=0.11.1,<0.12.0)", "sphinx-book-theme", "sphinx-panels (>=0.4.0,<0.5.0)", "sphinx-copybutton", "sphinx (>=2,<4)", "pyyaml"]
-testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions", "pytest-benchmark (>=3.2,<4.0)", "psutil"]
+benchmark = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.2,<4.0)", "mistune (>=0.8.4,<0.9.0)", "mistletoe-ebp (>=0.10.0,<0.11.0)", "panflute (>=1.12,<2.0)"]
+code_style = ["flake8 (>=3.7.0,<3.8.0)", "black (==19.10b0)", "pre-commit (==1.17.0)"]
+rtd = ["sphinx (>=2,<4)", "pyyaml", "sphinx-book-theme", "myst-nb", "sphinx-copybutton", "sphinx-panels (>=0.4.0,<0.5.0)"]
+testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
-version = "1.1.1"
+version = "2.0.1"
 description = "Safely add untrusted strings to HTML/XML markup."
 category = "dev"
 optional = false
-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*"
+python-versions = ">=3.6"
 
 [[package]]
 name = "mccabe"
@@ -282,21 +288,6 @@ category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "mdit-py-plugins"
-version = "0.2.6"
-description = "Collection of plugins for markdown-it-py"
-category = "dev"
-optional = false
-python-versions = "~=3.6"
-
-[package.dependencies]
-markdown-it-py = ">=0.5.8,<2.0.0"
-
-[package.extras]
-code_style = ["pre-commit (==2.6)"]
-testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"]
-
 [[package]]
 name = "mypy"
 version = "0.812"
@@ -323,29 +314,24 @@ python-versions = "*"
 
 [[package]]
 name = "myst-parser"
-version = "0.13.5"
+version = "0.8.2"
 description = "An extended commonmark compliant parser, with bridges to docutils & sphinx."
 category = "dev"
 optional = false
 python-versions = ">=3.6"
 
 [package.dependencies]
-docutils = ">=0.15"
-jinja2 = "*"
-markdown-it-py = ">=0.6.2,<0.7.0"
-mdit-py-plugins = ">=0.2.5,<0.3.0"
-pyyaml = "*"
-sphinx = ">=2,<4"
+markdown-it-py = ">=0.4.5,<0.5.0"
 
 [package.extras]
-code_style = ["flake8 (>=3.7.0,<3.8.0)", "black", "pre-commit (==1.17.0)"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
-rtd = ["sphinxcontrib-bibtex (<2.0.0)", "ipython", "sphinx-book-theme (>=0.0.36)", "sphinx-panels (>=0.5.2,<0.6.0)"]
-testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions", "beautifulsoup4"]
+code_style = ["black", "flake8 (>=3.7.0,<3.8.0)", "pre-commit (==1.17.0)"]
+rtd = ["ipython", "sphinx-book-theme", "sphinx-tabs", "sphinxcontrib-bibtex"]
+sphinx = ["docutils (>=0.15)", "pyyaml", "sphinx (>=2,<3)"]
+testing = ["beautifulsoup4", "coverage", "pytest-cov", "pytest-regressions", "pytest (>=3.6,<4)"]
 
 [[package]]
 name = "numpy"
-version = "1.20.1"
+version = "1.20.3"
 description = "NumPy is the fundamental package for array computing with Python."
 category = "main"
 optional = false
@@ -418,7 +404,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pyflakes"
-version = "2.3.0"
+version = "2.3.1"
 description = "passive checker of Python programs"
 category = "dev"
 optional = false
@@ -426,7 +412,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "pygments"
-version = "2.8.1"
+version = "2.9.0"
 description = "Pygments is a syntax highlighting package written in Python."
 category = "dev"
 optional = false
@@ -434,22 +420,19 @@ python-versions = ">=3.5"
 
 [[package]]
 name = "pylint"
-version = "2.7.2"
+version = "2.8.2"
 description = "python code static checker"
 category = "dev"
 optional = false
 python-versions = "~=3.6"
 
 [package.dependencies]
-astroid = ">=2.5.1,<2.6"
+astroid = ">=2.5.6,<2.7"
 colorama = {version = "*", markers = "sys_platform == \"win32\""}
 isort = ">=4.2.5,<6"
 mccabe = ">=0.6,<0.7"
 toml = ">=0.7.1"
 
-[package.extras]
-docs = ["sphinx (==3.5.1)", "python-docs-theme (==2020.12)"]
-
 [[package]]
 name = "pyparsing"
 version = "2.4.7"
@@ -460,7 +443,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "pytest"
-version = "6.2.2"
+version = "6.2.4"
 description = "pytest: simple powerful testing with Python"
 category = "dev"
 optional = false
@@ -482,14 +465,14 @@ testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "requests", "xm
 
 [[package]]
 name = "pytest-cov"
-version = "2.11.1"
+version = "2.12.0"
 description = "Pytest plugin for measuring coverage."
 category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
 [package.dependencies]
-coverage = ">=5.2.1"
+coverage = {version = ">=5.2.1", extras = ["toml"]}
 pytest = ">=4.6"
 
 [package.extras]
@@ -514,17 +497,9 @@ category = "main"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "pyyaml"
-version = "5.4.1"
-description = "YAML parser and emitter for Python"
-category = "dev"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*"
-
 [[package]]
 name = "regex"
-version = "2020.11.13"
+version = "2021.4.4"
 description = "Alternative regular expression module, to replace re."
 category = "dev"
 optional = false
@@ -550,7 +525,7 @@ socks = ["PySocks (>=1.5.6,!=1.5.7)", "win-inet-pton"]
 
 [[package]]
 name = "six"
-version = "1.15.0"
+version = "1.16.0"
 description = "Python 2 and 3 compatibility utilities"
 category = "main"
 optional = false
@@ -566,17 +541,17 @@ python-versions = "*"
 
 [[package]]
 name = "sphinx"
-version = "3.5.2"
+version = "4.0.2"
 description = "Python documentation generator"
 category = "dev"
 optional = false
-python-versions = ">=3.5"
+python-versions = ">=3.6"
 
 [package.dependencies]
 alabaster = ">=0.7,<0.8"
 babel = ">=1.3"
 colorama = {version = ">=0.3.5", markers = "sys_platform == \"win32\""}
-docutils = ">=0.12"
+docutils = ">=0.14,<0.18"
 imagesize = "*"
 Jinja2 = ">=2.3"
 packaging = "*"
@@ -597,11 +572,11 @@ test = ["pytest", "pytest-cov", "html5lib", "cython", "typed-ast"]
 
 [[package]]
 name = "sphinx-autodoc-typehints"
-version = "1.11.1"
+version = "1.12.0"
 description = "Type hints (PEP 484) support for the Sphinx autodoc extension"
 category = "dev"
 optional = false
-python-versions = ">=3.5.2"
+python-versions = ">=3.6"
 
 [package.dependencies]
 Sphinx = ">=3.0"
@@ -612,7 +587,7 @@ type_comments = ["typed-ast (>=1.4.0)"]
 
 [[package]]
 name = "sphinx-paramlinks"
-version = "0.5.0"
+version = "0.5.1"
 description = "Allows param links in Sphinx function/method descriptions to be linkable"
 category = "dev"
 optional = false
@@ -620,13 +595,14 @@ python-versions = "*"
 
 [[package]]
 name = "sphinx-rtd-theme"
-version = "0.5.1"
+version = "0.5.2"
 description = "Read the Docs theme for Sphinx"
 category = "dev"
 optional = false
 python-versions = "*"
 
 [package.dependencies]
+docutils = "<0.17"
 sphinx = "*"
 
 [package.extras]
@@ -705,7 +681,7 @@ test = ["pytest"]
 
 [[package]]
 name = "tifffile"
-version = "2021.3.16"
+version = "2021.4.8"
 description = "Read and write TIFF files"
 category = "main"
 optional = false
@@ -715,7 +691,7 @@ python-versions = ">=3.7"
 numpy = ">=1.15.1"
 
 [package.extras]
-all = ["imagecodecs (>=2021.1.11)", "matplotlib (>=3.2)", "lxml"]
+all = ["imagecodecs (>=2021.3.31)", "matplotlib (>=3.2)", "lxml"]
 
 [[package]]
 name = "toml"
@@ -727,7 +703,7 @@ python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 
 [[package]]
 name = "typed-ast"
-version = "1.4.2"
+version = "1.4.3"
 description = "a fork of Python 2 and 3 ast modules with type comment support"
 category = "dev"
 optional = false
@@ -735,7 +711,7 @@ python-versions = "*"
 
 [[package]]
 name = "typing-extensions"
-version = "3.7.4.3"
+version = "3.10.0.0"
 description = "Backported and Experimental Type Hints for Python 3.5+"
 category = "main"
 optional = false
@@ -783,7 +759,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
 
 [[package]]
 name = "xtiff"
-version = "0.7.1"
+version = "0.7.4"
 description = "A tiny Python library for writing multi-channel TIFF stacks"
 category = "main"
 optional = false
@@ -808,7 +784,7 @@ testing = ["pytest (>=4.6)", "pytest-checkdocs (>=1.2.3)", "pytest-flake8", "pyt
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+content-hash = "22a1df568772aab336ee56fdff8ca6d25ba2d12d6078ecdba3ec7ec7c71d47f8"
 
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@@ -916,129 +893,120 @@ docutils = [
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-    {file = "typing_extensions-3.7.4.3.tar.gz", hash = "sha256:99d4073b617d30288f569d3f13d2bd7548c3a7e4c8de87db09a9d29bb3a4a60c"},
+    {file = "typing_extensions-3.10.0.0-py2-none-any.whl", hash = "sha256:0ac0f89795dd19de6b97debb0c6af1c70987fd80a2d62d1958f7e56fcc31b497"},
+    {file = "typing_extensions-3.10.0.0-py3-none-any.whl", hash = "sha256:779383f6086d90c99ae41cf0ff39aac8a7937a9283ce0a414e5dd782f4c94a84"},
+    {file = "typing_extensions-3.10.0.0.tar.gz", hash = "sha256:50b6f157849174217d0656f99dc82fe932884fb250826c18350e159ec6cdf342"},
 ]
 urllib3 = [
     {file = "urllib3-1.26.4-py2.py3-none-any.whl", hash = "sha256:2f4da4594db7e1e110a944bb1b551fdf4e6c136ad42e4234131391e21eb5b0df"},
@@ -1353,8 +1299,8 @@ xmltodict = [
     {file = "xmltodict-0.12.0.tar.gz", hash = "sha256:50d8c638ed7ecb88d90561beedbf720c9b4e851a9fa6c47ebd64e99d166d8a21"},
 ]
 xtiff = [
-    {file = "xtiff-0.7.1-py3-none-any.whl", hash = "sha256:9217e047fa26592b1c0610cb8ac437de1c5af267df4f272102f6a3747d0daa69"},
-    {file = "xtiff-0.7.1.tar.gz", hash = "sha256:c7041f29bebc2af912563fae4d3fec5e4a5978669f20e7f3498da9b151a316c9"},
+    {file = "xtiff-0.7.4-py3-none-any.whl", hash = "sha256:794335eb2ca7486384422f56d416004b8e0719092dc7cd1581b428536945180a"},
+    {file = "xtiff-0.7.4.tar.gz", hash = "sha256:795939018aa0907e5b9b475bdb72fe5ec63118759b86072e465b746bdb66cf82"},
 ]
 zipp = [
     {file = "zipp-3.4.1-py3-none-any.whl", hash = "sha256:51cb66cc54621609dd593d1787f286ee42a5c0adbb4b29abea5a63edc3e03098"},
diff --git a/pyproject.toml b/pyproject.toml
index abfeea3..050ba61 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "imctools"
-version = "2.1.6"
+version = "2.1.7"
 description = "Tools to handle Fluidigm IMC data"
 license = "MIT"
 authors = ["Vito Zanotelli <vito.zanotelli@uzh.ch>", "Anton Rau <anton.rau@uzh.ch>"]
@@ -30,7 +30,7 @@ packaging = "*"
 pandas = "*"
 typing_extensions = ">=3.7.4.3"
 xmltodict = ">=0.12.0"
-xtiff = ">=0.7.1"
+xtiff = ">=0.7.4"
 
 [tool.poetry.dev-dependencies]
 autoflake = "*"