diff --git a/.idea/.gitignore b/.idea/.gitignore
new file mode 100644
index 0000000000000000000000000000000000000000..26d33521af10bcc7fd8cea344038eaaeb78d0ef5
--- /dev/null
+++ b/.idea/.gitignore
@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml
diff --git a/.idea/inspectionProfiles/profiles_settings.xml b/.idea/inspectionProfiles/profiles_settings.xml
new file mode 100644
index 0000000000000000000000000000000000000000..105ce2da2d6447d11dfe32bfb846c3d5b199fc99
--- /dev/null
+++ b/.idea/inspectionProfiles/profiles_settings.xml
@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>
\ No newline at end of file
diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
index 0000000000000000000000000000000000000000..d1e22ecb89619a9c2dcf51a28d891a196d2462a0
--- /dev/null
+++ b/.idea/misc.xml
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8" project-jdk-type="Python SDK" />
+</project>
\ No newline at end of file
diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
index 0000000000000000000000000000000000000000..bda99c39b8a075ca10211de01f45aba3053bdaeb
--- /dev/null
+++ b/.idea/modules.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/nd2shrink.iml" filepath="$PROJECT_DIR$/.idea/nd2shrink.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file
diff --git a/.idea/nd2shrink.iml b/.idea/nd2shrink.iml
new file mode 100644
index 0000000000000000000000000000000000000000..4f2c9af68e19e4eec1ff1bdfe7a553e2ed3b5078
--- /dev/null
+++ b/.idea/nd2shrink.iml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+  <component name="TestRunnerService">
+    <option name="PROJECT_TEST_RUNNER" value="pytest" />
+  </component>
+</module>
\ No newline at end of file
diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000000000000000000000000000000000000..94a25f7f4cb416c083d265558da75d457237d671
--- /dev/null
+++ b/.idea/vcs.xml
@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 25c729f58877eaa31f0a4fad45ff9314dd81b79d..fb1cda21619889e7cce222b2319719ba17e58405 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -1,3 +1,6 @@
 {
-    "python.pythonPath": "/bin/python3"
+    "python.pythonPath": "/bin/python3",
+    "restructuredtext.confPath": "${workspaceFolder}/source",
+    "esbonio.server.enabled": true,
+    "esbonio.sphinx.confDir": "${workspaceFolder}/source"
 }
\ No newline at end of file
diff --git a/=0.1.0 b/=0.1.0
new file mode 100644
index 0000000000000000000000000000000000000000..0744665184eb1bbb1d6a0553776ddc3e44cd16e9
--- /dev/null
+++ b/=0.1.0
@@ -0,0 +1,18 @@
+Collecting jupyter-telemetry
+  Downloading jupyter_telemetry-0.1.0-py3-none-any.whl (7.1 kB)
+Requirement already satisfied, skipping upgrade: jsonschema in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-telemetry) (3.2.0)
+Requirement already satisfied, skipping upgrade: traitlets in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-telemetry) (5.0.5)
+Requirement already satisfied, skipping upgrade: ruamel.yaml in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-telemetry) (0.16.12)
+Requirement already satisfied, skipping upgrade: python-json-logger in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jupyter-telemetry) (2.0.1)
+Requirement already satisfied, skipping upgrade: pyrsistent>=0.14.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema->jupyter-telemetry) (0.17.3)
+Requirement already satisfied, skipping upgrade: setuptools in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema->jupyter-telemetry) (50.3.0.post20201006)
+Requirement already satisfied, skipping upgrade: attrs>=17.4.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema->jupyter-telemetry) (20.2.0)
+Requirement already satisfied, skipping upgrade: six>=1.11.0 in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from jsonschema->jupyter-telemetry) (1.15.0)
+Requirement already satisfied, skipping upgrade: ipython-genutils in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from traitlets->jupyter-telemetry) (0.2.0)
+Requirement already satisfied, skipping upgrade: ruamel.yaml.clib>=0.1.2; platform_python_implementation == "CPython" and python_version < "3.9" in /home/aaristov/miniconda3/envs/nd2/lib/python3.8/site-packages (from ruamel.yaml->jupyter-telemetry) (0.2.2)
+Installing collected packages: jupyter-telemetry
+  Attempting uninstall: jupyter-telemetry
+    Found existing installation: jupyter-telemetry 0.0.5
+    Uninstalling jupyter-telemetry-0.0.5:
+      Successfully uninstalled jupyter-telemetry-0.0.5
+Successfully installed jupyter-telemetry-0.1.0
diff --git a/Makefile b/Makefile
new file mode 100644
index 0000000000000000000000000000000000000000..b97de95f5534e90e734d203026166ebd621f4cfd
--- /dev/null
+++ b/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     = docs
+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)
diff --git a/Snakefile b/Snakefile
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/docs/api.rst b/docs/api.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0c80c31f38555b635437405a6445bbff3bb22b41
--- /dev/null
+++ b/docs/api.rst
@@ -0,0 +1,22 @@
+API
+===
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+   
+   droplet_growth
+
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   nd2tif
+   
+.. autosummary::
+   :toctree: generated
+   :recursive:
+
+   segment
+   
+   
\ No newline at end of file
diff --git a/docs/conf.py b/docs/conf.py
new file mode 100644
index 0000000000000000000000000000000000000000..60b78dc97f89234aeea2e7e1d60a11fc8bf04c80
--- /dev/null
+++ b/docs/conf.py
@@ -0,0 +1,59 @@
+# 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('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+import sphinx
+
+
+project = 'Multidroplet-chip'
+copyright = '2022, Andrey Aristov'
+author = 'Andrey Aristov'
+
+# The full version, including alpha/beta/rc tags
+release = '0.1.5'
+
+
+# -- 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',
+'sphinx.ext.autosummary',
+]
+
+# 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 -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# 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']
\ No newline at end of file
diff --git a/docs/generated/droplet_growth.count.rst b/docs/generated/droplet_growth.count.rst
new file mode 100644
index 0000000000000000000000000000000000000000..657e0dc93e70180a51328295d8f7e5640370772a
--- /dev/null
+++ b/docs/generated/droplet_growth.count.rst
@@ -0,0 +1,35 @@
+droplet\_growth.count
+=====================
+
+.. automodule:: droplet_growth.count
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      crop
+      gdif
+      get_n_cells
+      get_peak_number
+      get_peaks_all_wells
+      get_peaks_per_frame
+      peak_local_max_labels
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.fit.rst b/docs/generated/droplet_growth.fit.rst
new file mode 100644
index 0000000000000000000000000000000000000000..bde199f86aced1b63b579705a662652f00fdf5f5
--- /dev/null
+++ b/docs/generated/droplet_growth.fit.rst
@@ -0,0 +1,48 @@
+droplet\_growth.fit
+===================
+
+.. automodule:: droplet_growth.fit
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      add_doubling_time
+      erf_fun
+      exp_exp_fit
+      exp_exp_fun
+      exp_on_baseline
+      exponent
+      fit_exp_on_baseline
+      fit_exponent
+      fit_sigmoid
+      gompertz
+      hill
+      lag_exponent
+      lin_exp_fit
+      lin_exp_fun
+      plot_fit
+      prob_survive
+      show_probs
+      sigmoid
+      single_prob
+      single_prob_to_final_states
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.mic.rst b/docs/generated/droplet_growth.mic.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8b8d44972e5a4347b8e403cb40482279a3d4e9e2
--- /dev/null
+++ b/docs/generated/droplet_growth.mic.rst
@@ -0,0 +1,39 @@
+droplet\_growth.mic
+===================
+
+.. automodule:: droplet_growth.mic
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      align_and_count
+      concatenate_horizontally_results_for_one_chip
+      concatenate_vertically_all_chips_csv
+      get_cell_numbers
+      get_file_pair
+      get_intensities
+      get_overnight_intensities
+      get_stats
+      read_align_count
+      show_mean_instensities
+      show_prob_survive
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.multiwell.rst b/docs/generated/droplet_growth.multiwell.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0337ba9e98288bebefc327250b2fae189a6b98ef
--- /dev/null
+++ b/docs/generated/droplet_growth.multiwell.rst
@@ -0,0 +1,43 @@
+droplet\_growth.multiwell
+=========================
+
+.. automodule:: droplet_growth.multiwell
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      analyse_curves
+      estimate_bg
+      filter_table_by_max_intensity
+      filter_table_by_min_intensity
+      get_2d_gradient
+      get_background_table
+      get_centers
+      get_intensity_table
+      get_mask
+      get_outlines
+      plot_intensity_line
+      plot_intensity_raw_line
+      plot_intensity_vs_time
+      read_stitched_nd2
+      show
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.poisson.rst b/docs/generated/droplet_growth.poisson.rst
new file mode 100644
index 0000000000000000000000000000000000000000..e480fb53e93c0ed7f8b021e0527fab5a3e308438
--- /dev/null
+++ b/docs/generated/droplet_growth.poisson.rst
@@ -0,0 +1,29 @@
+droplet\_growth.poisson
+=======================
+
+.. automodule:: droplet_growth.poisson
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      fit
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.projections.rst b/docs/generated/droplet_growth.projections.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c5fc389bb8f3dfa4d9de836aca50526a15fed5d8
--- /dev/null
+++ b/docs/generated/droplet_growth.projections.rst
@@ -0,0 +1,32 @@
+droplet\_growth.projections
+===========================
+
+.. automodule:: droplet_growth.projections
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      crop
+      get_max_mean_projections
+      get_t_series
+      save_projections
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.register.rst b/docs/generated/droplet_growth.register.rst
new file mode 100644
index 0000000000000000000000000000000000000000..717c1da13c2ad7f62b3e224e99aa6c6bc81f0f3a
--- /dev/null
+++ b/docs/generated/droplet_growth.register.rst
@@ -0,0 +1,43 @@
+droplet\_growth.register
+========================
+
+.. automodule:: droplet_growth.register
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      align_mask_to_bf
+      align_stack
+      align_stack_nd
+      align_timelapse
+      calculate_padding
+      fft_mask
+      filter_by_fft
+      get_fft_size
+      get_transform
+      increase
+      pad
+      register
+      scale_tvec
+      transform
+      unpad
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/droplet_growth.rst b/docs/generated/droplet_growth.rst
new file mode 100644
index 0000000000000000000000000000000000000000..9863cfdf8f2d297ae62dcf2c73c454ac6e44707e
--- /dev/null
+++ b/docs/generated/droplet_growth.rst
@@ -0,0 +1,38 @@
+droplet\_growth
+===============
+
+.. automodule:: droplet_growth
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   droplet_growth.count
+   droplet_growth.fit
+   droplet_growth.mic
+   droplet_growth.multiwell
+   droplet_growth.poisson
+   droplet_growth.projections
+   droplet_growth.register
+   droplet_growth.segment
+
diff --git a/docs/generated/droplet_growth.segment.rst b/docs/generated/droplet_growth.segment.rst
new file mode 100644
index 0000000000000000000000000000000000000000..505aea06b298f73c58717ad1ed1fd3a4fe209cf4
--- /dev/null
+++ b/docs/generated/droplet_growth.segment.rst
@@ -0,0 +1,31 @@
+droplet\_growth.segment
+=======================
+
+.. automodule:: droplet_growth.segment
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      filter_mask
+      get_local_otsu
+      get_mask
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/nd2tif.read.rst b/docs/generated/nd2tif.read.rst
new file mode 100644
index 0000000000000000000000000000000000000000..a2a9353815f4c50dc61c54a54c86053cc10d7c6a
--- /dev/null
+++ b/docs/generated/nd2tif.read.rst
@@ -0,0 +1,31 @@
+nd2tif.read
+===========
+
+.. automodule:: nd2tif.read
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      auto_order
+      nd2
+      tiff
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/nd2tif.rst b/docs/generated/nd2tif.rst
new file mode 100644
index 0000000000000000000000000000000000000000..8672a58ac83f2db12e8b9f9deb2ec7a0f58c29f9
--- /dev/null
+++ b/docs/generated/nd2tif.rst
@@ -0,0 +1,33 @@
+nd2tif
+======
+
+.. automodule:: nd2tif
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   nd2tif.read
+   nd2tif.save
+   nd2tif.transform
+
diff --git a/docs/generated/nd2tif.save.rst b/docs/generated/nd2tif.save.rst
new file mode 100644
index 0000000000000000000000000000000000000000..609f85da5d5d21d373057e155eb9e335d98cdf67
--- /dev/null
+++ b/docs/generated/nd2tif.save.rst
@@ -0,0 +1,29 @@
+nd2tif.save
+===========
+
+.. automodule:: nd2tif.save
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      tiff
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/nd2tif.transform.rst b/docs/generated/nd2tif.transform.rst
new file mode 100644
index 0000000000000000000000000000000000000000..01d103688da90c58e6ab3a05fd3279708b2fc8f8
--- /dev/null
+++ b/docs/generated/nd2tif.transform.rst
@@ -0,0 +1,40 @@
+nd2tif.transform
+================
+
+.. automodule:: nd2tif.transform
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      recursive_downscale
+      reshape_like_IJ
+      scale_down
+      shape
+      to_8bits
+   
+   
+
+   
+   
+   .. rubric:: Classes
+
+   .. autosummary::
+   
+      ImageJStack
+      Well
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/segment.muvicyte.rst b/docs/generated/segment.muvicyte.rst
new file mode 100644
index 0000000000000000000000000000000000000000..0a6a4d76552a9bc6d6bffd7d82e2bcf9c948d513
--- /dev/null
+++ b/docs/generated/segment.muvicyte.rst
@@ -0,0 +1,41 @@
+segment.muvicyte
+================
+
+.. automodule:: segment.muvicyte
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      get_biggest_region
+      get_channels
+      get_contour
+      get_grouped_paths
+      get_max_pos2D
+      get_maxima
+      move_to_center
+      process_dataset
+      rotate
+      rotate_organoid
+      segment_bf
+      segment_jpg
+      sub_bg
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/generated/segment.rst b/docs/generated/segment.rst
new file mode 100644
index 0000000000000000000000000000000000000000..236e11634f9abbf64f80e9f8606ad4124932c9d2
--- /dev/null
+++ b/docs/generated/segment.rst
@@ -0,0 +1,32 @@
+segment
+=======
+
+.. automodule:: segment
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+
+   segment.muvicyte
+   segment.seg
+
diff --git a/docs/generated/segment.seg.rst b/docs/generated/segment.seg.rst
new file mode 100644
index 0000000000000000000000000000000000000000..6bc52855f08a44c79160cfd35c3a18e8cc3935a5
--- /dev/null
+++ b/docs/generated/segment.seg.rst
@@ -0,0 +1,29 @@
+segment.seg
+===========
+
+.. automodule:: segment.seg
+
+   
+   
+   
+
+   
+   
+   .. rubric:: Functions
+
+   .. autosummary::
+   
+      crop_center
+   
+   
+
+   
+   
+   
+
+   
+   
+   
+
+
+
diff --git a/docs/index.rst b/docs/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..1c9e251931db543b3e9755fdcf8e70d9acdbc355
--- /dev/null
+++ b/docs/index.rst
@@ -0,0 +1,23 @@
+.. Multidroplet-chip documentation master file, created by
+   sphinx-quickstart on Tue Feb  1 19:35:37 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to Multidroplet-chip's documentation!
+=============================================
+
+.. toctree::
+   :maxdepth: 3
+   :caption: Contents:
+
+   usage
+   api
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
diff --git a/docs/usage.rst b/docs/usage.rst
new file mode 100644
index 0000000000000000000000000000000000000000..29625ab44a0dadbb8773c9f9bbfed11e80844611
--- /dev/null
+++ b/docs/usage.rst
@@ -0,0 +1,30 @@
+Installation
+============
+
+Clone the repository from git 
+
+.. code-block:: console 
+
+    git clone https://gitlab.pasteur.fr/aaristov/nd2shrink.git
+    git checkout Develop-multiwell-analysis
+
+and run 
+
+.. code-block:: console 
+
+    cd nd2shrink
+    pip install .
+
+
+Usage
+=====
+
+.. code-block:: python
+
+    import tifffile as tf
+    from droplet-growth import register
+    
+    template = tf.imread('path_to_template')
+    mask = tf.imread('path_to_mask')
+
+    aligned_stack = register.aligned_stack(path_to_bf_fluo_stack, template, mask)
\ No newline at end of file
diff --git a/droplet_growth/__init__.py b/droplet_growth/__init__.py
index 9022a4b969e269a5038ce8f8c2f1e3d8ce9c66ae..696a3b32a4eb59ab47bcaadfb720537983d9e9e7 100644
--- a/droplet_growth/__init__.py
+++ b/droplet_growth/__init__.py
@@ -1 +1,3 @@
+__version__=0.
+
 from droplet_growth import register
\ No newline at end of file
diff --git a/droplet_growth/register.py b/droplet_growth/register.py
index a064b6d53792e318978adc14dfa790f5a9b2de07..8634ba25ea4e1d9e1fa1df278ccfd833289e191c 100644
--- a/droplet_growth/register.py
+++ b/droplet_growth/register.py
@@ -32,6 +32,11 @@ def align_stack(data_or_path, template16, mask2, plot=False, path=None, binnings
     When the transformation verctor will be applied to the original data and stacked with the mask.
     The output stack is of the same size as mask.
     The resulting 3-layer stack will be returned and also saved with suffix ".aligned.tif"
+    
+
+    :return: aligned (bf, fluo, mask)
+    :rtype: np.ndarray
+    
     '''
     if isinstance(data_or_path, str):
         path = data_or_path
diff --git a/make.bat b/make.bat
new file mode 100644
index 0000000000000000000000000000000000000000..6fcf05b4b76f8b9774c317ac8ada402f8a7087de
--- /dev/null
+++ b/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.https://www.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
diff --git a/multiwell-0811.ipynb b/multiwell-0811.ipynb
index 9f30844f85f4e86f57cfbd0c5f208cc954a3e494..562bb9269a18326c2334013db6f38f0437dfec55 100644
--- a/multiwell-0811.ipynb
+++ b/multiwell-0811.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -20,7 +20,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 6,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -38,7 +38,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 7,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +47,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 8,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -56,16 +56,16 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 9,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'3.8.3 (default, May 19 2020, 18:47:26) \\n[GCC 7.3.0]'"
+       "'3.8.5 (default, Sep  4 2020, 07:30:14) \\n[GCC 7.3.0]'"
       ]
      },
-     "execution_count": 5,
+     "execution_count": 9,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -77,7 +77,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 10,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -88,7 +88,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 11,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -100,7 +100,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 12,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -109,7 +109,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 13,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -18200,7 +18200,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.3"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,
diff --git a/segment/muvicyte.py b/segment/muvicyte.py
index e5346d84a364ad0d5072154168bcb1f929ffa488..81cd34aeb668cac7d09ffda86c03c5548d3ad77b 100644
--- a/segment/muvicyte.py
+++ b/segment/muvicyte.py
@@ -7,7 +7,7 @@ from nd2tif.transform import Well
 import os
 import pandas as pd
 from PIL import Image
-from scipy.ndimage import gaussian_filter1d
+from scipy.ndimage import gaussian_filter1d, gaussian_filter
 from segment import seg
 from skimage.color import label2rgb
 from skimage.transform import rotate as _rotate