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