diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index dd84ea7..0000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,38 +0,0 @@ ---- -name: Bug report -about: Create a report to help us improve -title: '' -labels: '' -assignees: '' - ---- - -**Describe the bug** -A clear and concise description of what the bug is. - -**To Reproduce** -Steps to reproduce the behavior: -1. Go to '...' -2. Click on '....' -3. Scroll down to '....' -4. See error - -**Expected behavior** -A clear and concise description of what you expected to happen. - -**Screenshots** -If applicable, add screenshots to help explain your problem. - -**Desktop (please complete the following information):** - - OS: [e.g. iOS] - - Browser [e.g. chrome, safari] - - Version [e.g. 22] - -**Smartphone (please complete the following information):** - - Device: [e.g. iPhone6] - - OS: [e.g. iOS8.1] - - Browser [e.g. stock browser, safari] - - Version [e.g. 22] - -**Additional context** -Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index bbcbbe7..0000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for this project -title: '' -labels: '' -assignees: '' - ---- - -**Is your feature request related to a problem? Please describe.** -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] - -**Describe the solution you'd like** -A clear and concise description of what you want to happen. - -**Describe alternatives you've considered** -A clear and concise description of any alternative solutions or features you've considered. - -**Additional context** -Add any other context or screenshots about the feature request here. diff --git a/.github/workflows/codeql-analysis.yml b/.github/workflows/codeql-analysis.yml deleted file mode 100644 index 1326703..0000000 --- a/.github/workflows/codeql-analysis.yml +++ /dev/null @@ -1,70 +0,0 @@ -# For most projects, this workflow file will not need changing; you simply need -# to commit it to your repository. -# -# You may wish to alter this file to override the set of languages analyzed, -# or to provide custom queries or build logic. -# -# ******** NOTE ******** -# We have attempted to detect the languages in your repository. Please check -# the `language` matrix defined below to confirm you have the correct set of -# supported CodeQL languages. -# -name: "CodeQL" - -on: - push: - branches: [ main ] - pull_request: - # The branches below must be a subset of the branches above - branches: [ main ] - schedule: - - cron: '39 9 * * 3' - -jobs: - analyze: - name: Analyze - runs-on: ubuntu-latest - permissions: - actions: read - contents: read - security-events: write - - strategy: - fail-fast: false - matrix: - language: [ 'python' ] - # CodeQL supports [ 'cpp', 'csharp', 'go', 'java', 'javascript', 'python', 'ruby' ] - # Learn more about CodeQL language support at https://git.io/codeql-language-support - - steps: - - name: Checkout repository - uses: actions/checkout@v2 - - # Initializes the CodeQL tools for scanning. - - name: Initialize CodeQL - uses: github/codeql-action/init@v1 - with: - languages: ${{ matrix.language }} - # If you wish to specify custom queries, you can do so here or in a config file. - # By default, queries listed here will override any specified in a config file. - # Prefix the list here with "+" to use these queries and those in the config file. - # queries: ./path/to/local/query, your-org/your-repo/queries@main - - # Autobuild attempts to build any compiled languages (C/C++, C#, or Java). - # If this step fails, then you should remove it and run the build manually (see below) - - name: Autobuild - uses: github/codeql-action/autobuild@v1 - - # ℹ️ Command-line programs to run using the OS shell. - # 📚 https://git.io/JvXDl - - # ✏️ If the Autobuild fails above, remove it and uncomment the following three lines - # and modify them (or add more) to build your code if your project - # uses a compiled language - - #- run: | - # make bootstrap - # make release - - - name: Perform CodeQL Analysis - uses: github/codeql-action/analyze@v1 diff --git a/.gitignore b/.gitignore deleted file mode 100644 index 75bcb87..0000000 --- a/.gitignore +++ /dev/null @@ -1,140 +0,0 @@ -# Byte-compiled / optimized / DLL files -__pycache__/ -*.py[cod] -*$py.class - -# C extensions -*.so - -# Distribution / packaging -.Python -build/ -develop-eggs/ -dist/ -downloads/ -eggs/ -.eggs/ -lib/ -lib64/ -parts/ -sdist/ -var/ -wheels/ -pip-wheel-metadata/ -share/python-wheels/ -*.egg-info/ -.installed.cfg -*.egg -MANIFEST - -# PyInstaller -# Usually these files are written by a python script from a template -# before PyInstaller builds the exe, so as to inject date/other infos into it. -*.manifest -*.spec - -# Installer logs -pip-log.txt -pip-delete-this-directory.txt - -# Unit test / coverage reports -htmlcov/ -.tox/ -.nox/ -.coverage -.coverage.* -.cache -nosetests.xml -coverage.xml -*.cover -*.py,cover -.hypothesis/ -.pytest_cache/ - -# Translations -*.mo -*.pot - -# Django stuff: -*.log -local_settings.py -db.sqlite3 -db.sqlite3-journal - -# Flask stuff: -instance/ -.webassets-cache - -# Scrapy stuff: -.scrapy - -# Sphinx documentation -docs/_build/ - -# PyBuilder -target/ - -# Jupyter Notebook -.ipynb_checkpoints - -# IPython -profile_default/ -ipython_config.py - -# pyenv -.python-version - -# pipenv -# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control. -# However, in case of collaboration, if having platform-specific dependencies or dependencies -# having no cross-platform support, pipenv may install dependencies that don't work, or not -# install all needed dependencies. -#Pipfile.lock - -# PEP 582; used by e.g. github.com/David-OConnor/pyflow -__pypackages__/ - -# Celery stuff -celerybeat-schedule -celerybeat.pid - -# SageMath parsed files -*.sage.py - -# Environments -.env -.venv -env/ -venv/ -ENV/ -env.bak/ -venv.bak/ - -# Spyder project settings -.spyderproject -.spyproject - -# Rope project settings -.ropeproject - -# mkdocs documentation -/site - -# mypy -.mypy_cache/ -.dmypy.json -dmypy.json - -# Pyre type checker -.pyre/ - -# mac -.DS_Store - -# files -*.vtk -*.vtp -*.m4v - -# test -*test* diff --git a/.gitmodules b/.gitmodules deleted file mode 100644 index 3cd0dc2..0000000 --- a/.gitmodules +++ /dev/null @@ -1,3 +0,0 @@ -[submodule "FearlessHearts"] - path = FearlessHearts - url = https://github.com/marcomusy/FearlessHearts.git diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md deleted file mode 100644 index 0f5146b..0000000 --- a/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,128 +0,0 @@ -# Contributor Covenant Code of Conduct - -## Our Pledge - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, -nationality, personal appearance, race, religion, or sexual identity -and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -## Our Standards - -Examples of behavior that contributes to a positive environment for our -community include: - -* Demonstrating empathy and kindness toward other people -* Being respectful of differing opinions, viewpoints, and experiences -* Giving and gracefully accepting constructive feedback -* Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -* Focusing on what is best not just for us as individuals, but for the - overall community - -Examples of unacceptable behavior include: - -* The use of sexualized language or imagery, and sexual attention or - advances of any kind -* Trolling, insulting or derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or email - address, without their explicit permission -* Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Enforcement Responsibilities - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, -or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -## Scope - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at -gio.dalmasso@gmail.com. -All complaints will be reviewed and investigated promptly and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -## Enforcement Guidelines - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -### 1. Correction - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -### 2. Warning - -**Community Impact**: A violation through a single incident or series -of actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or -permanent ban. - -### 3. Temporary Ban - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -### 4. Permanent Ban - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within -the community. - -## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], -version 2.0, available at -https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. - -Community Impact Guidelines were inspired by [Mozilla's code of conduct -enforcement ladder](https://github.com/mozilla/diversity). - -[homepage]: https://www.contributor-covenant.org - -For answers to common questions about this code of conduct, see the FAQ at -https://www.contributor-covenant.org/faq. Translations are available at -https://www.contributor-covenant.org/translations. diff --git a/Fearless/computeAllIntesities.py b/Fearless/computeAllIntesities.py deleted file mode 100644 index b3f4c75..0000000 --- a/Fearless/computeAllIntesities.py +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env python -# -# @Author: Giovanni Dalmasso -# @Date: 11-Jan-2022 -# @Email: giovanni.dalmasso@embl.es -# @Project: FeARLesS -# @Filename: computeAllIntesities.py -# @Last modified by: gio -# @Last modified time: 02-May-2022 -# @License: MIT -# @Copyright: Copyright © 2021 Giovanni Dalmasso - - -from vedo import printc, load, ProgressBar - -from utils import pathExists, voxelIntensity -import numpy as np - - -radiusDiscretisation = 50 -N = 250 -FFTexpansion = radiusDiscretisation -expo = 1.0 - - -DataPath = '../data/Limbs_Flank/' -path_results = 'res/' \ - 'allIntensities-sampleSize100-' + \ - 'radiusDiscretisation-' + \ - str(radiusDiscretisation) + '-N-' + str(N) + '/' - - -pathExists(path_results) - - -limbs = [2490, 2500, 2510, 2540, 2570, 2571, 2573, 2574, 2590, 2600, 2601, 2610, 2620, 2631, 2640, 2642, 2650, 2651, 2652, 2653, 2654, 2655, 2660, - 2662, 2663, 2671, 2681, 2682, 2690, 2700, 2701, 2703, 2704, 2710, 2711, 2712, 2714, 2720, 2721, 2722, 2731, 2732, 2740, 2741, 2742, 2745, - 2746, 2750, 2751, 2752, 2754, 2755, 2760, 2761, 2762, 2771, 2772, 2780, 2790, 2831, 2840, 2850, 2870, 2880, 2881, 2882, 2890, 2901, 2902] -t = [249, 250, 251, 254, 257, 257, 257, 257, 259, 260, 260, 261, 262, 263, 264, 264, 265, 265, 265, 265, 265, 265, 266, 266, 266, 267, - 268, 268, 269, 270, 270, 270, 270, 271, 271, 271, 271, 272, 272, 272, 273, 273, 274, 274, 274, 274, 274, 275, 275, 275, 275, 275, 276, 276, 276, - 277, 277, 278, 279, 283, 284, 285, 287, 288, 288, 288, 289, 290, 290] - -Treal = np.arange(t[0], t[-1]+1, dtype=int) -newTotLimbs = len(Treal) - -totlimbs = len(limbs) -print(totlimbs, 'limbs!! \n') - - -pb = ProgressBar(0, totlimbs, c=5) -for j in pb.range(): - - ############################################## - # loading files - vol = load(DataPath + 'ReferenceShape_' + - str(limbs[j])[0:-1] + '_' + str(limbs[j])[-1] + '.vti') - - ############################################## - # computing voxel intensities - allIntensities = voxelIntensity(vol, expo, N, radiusDiscretisation) - - name = 'allIntensities_' + 'ReferenceShape_' + \ - str(limbs[j])[0:-1] + '_' + str(limbs[j])[-1] - np.save(path_results + name, allIntensities) - printc('allIntensities', name, 'saved!', c='g') - - allIntensitiesShape = allIntensities.shape - np.save(path_results + 'allIntensitiesShape', allIntensitiesShape) - - pb.print() diff --git a/Fearless/makeVoxel.py b/Fearless/makeVoxel.py deleted file mode 100644 index 46ba754..0000000 --- a/Fearless/makeVoxel.py +++ /dev/null @@ -1,91 +0,0 @@ -#!/usr/bin/env python -# -# @Author: Giovanni Dalmasso -# @Date: 13-Jan-2022 -# @Email: giovanni.dalmasso@embl.es -# @Project: FeARLesS -# @Filename: makeVoxel.py -# @Last modified by: gio -# @Last modified time: 02-May-2022 -# @License: MIT -# @Copyright: Copyright © 2021 Giovanni Dalmasso - - -from utils import pathExists -from vedo import ProgressBar, load, printc, volumeFromMesh, write -import numpy as np - - -"""Convert a vtk mesh from the limb-data files into voxel data.""" - - -DataPath = 'limbs+flank/' - - -limbs = load(DataPath + '*.vtk') -totLimbs = len(limbs) -printc("limbs # ", totLimbs, invert=1) - - -sampleSize = (100, 100, 100) - -path_results = 'res/TIF-signedDist_sampleSize' + \ - str(sampleSize[0]) + '/' - -pathExists(path_results) - -# needed to have all the normals pointing in the same direction -noMirror = [4, 5, 6, 8, 9, 13, 14, 16, 17, 18, 19, 20, 22, 23, 25, 26, 27, 29, 30, 31, 33, 34, - 35, 37, 38, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 52, 53, 55, 56, 59, 63, 64, 67, 68] - -# collecting imgBounds of all limbs -allBounds = np.empty(shape=(6, totLimbs)) -pb = ProgressBar(0, totLimbs, c=1) -for j in pb.range(): - allBounds[:, j] = limbs[j].GetBounds() - pb.print('all bounds ...') - -# finding max imgBounds -allBoundsTmp = [] -pb = ProgressBar(0, allBounds.shape[0], c=1) -for j in pb.range(): - if allBounds[j, 0] > 0: - allBoundsTmp.append(np.max(allBounds[j, :])) - else: - allBoundsTmp.append(np.min(allBounds[j, :])) - pb.print('allBoundsTmp ... ') - -# making imgBounds a bit bigger, just in case -imgBOunds = [x * 1.2 for x in allBoundsTmp] - - -pb = ProgressBar(0, totLimbs, c=1) -for j in pb.range(): - - time = limbs[j].filename.split('.')[0].split('/')[-1].split('_')[1] - - if limbs[j].filename.split('.')[0].split('/')[-1].split('_')[-1] == 'clean-newAlignement': - outputName = path_results + 'ReferenceShape_' + time + '_0.vti' - else: - outputName = path_results + 'ReferenceShape_' + time + '_' + \ - limbs[j].filename.split('.')[0].split( - '/')[-1].split('_')[-1] + '.vti' - - if j in noMirror: - vol = volumeFromMesh(limbs[j], - dims=sampleSize, - bounds=imgBOunds, - signed=True, - negate=True, # invert sign - ) - write(vol, outputName) - else: - vol = volumeFromMesh(limbs[j], - dims=sampleSize, - bounds=imgBOunds, - signed=True, - negate=False, # invert sign - ) - write(vol, outputName) - - pb.print('making voxel data ...') diff --git a/Fearless/morphing.py b/Fearless/morphing.py deleted file mode 100644 index e109eb3..0000000 --- a/Fearless/morphing.py +++ /dev/null @@ -1,185 +0,0 @@ -#!/usr/bin/env python -# -# @Author: Giovanni Dalmasso -# @Date: 20-Jan-2022 -# @Email: giovanni.dalmasso@embl.es -# @Project: FeARLesS -# @Filename: morphing.py -# @Last modified by: gio -# @Last modified time: 02-May-2022 -# @License: MIT -# @Copyright: Copyright © 2021 Giovanni Dalmasso - - -import numpy as np -from vedo import printc, ProgressBar, load, Points, write, interpolateToVolume -from utils import pathExists, forwardTransformation, samplePoints, inverseTransformations - - -##################################### -# PARAMETERS -sampleSize = 100 -radiusDiscretisation = 50 -N = 250 -lmax = 50 -expo = 1.0 -deg_fit = 6 - -printc('\n sampleSize', sampleSize, '- radiusDiscretisation', - radiusDiscretisation, '- N', N, '- lmax', lmax, - c='green') - - -path = 'res/' \ - 'allIntensities-sampleSize100-' + \ - 'radiusDiscretisation-' + \ - str(radiusDiscretisation) + '-N-' + str(N) + '/' -path_resultsCLM = 'res/' \ - '/CLM/'\ - 'morphing_sampleSize' + str(sampleSize) + \ - '-radDisc' + str(radiusDiscretisation) + '-N' + str(N) + '-degFit' + \ - str(deg_fit) + '-lmax'+str(lmax) + '/' -path_results = 'res/' \ - 'morphing_sampleSize' \ - + str(sampleSize) + \ - '-radDisc' + str(radiusDiscretisation) + '-N' + str(N) + '-degFit' + \ - str(deg_fit) + '-lmax'+str(lmax) + '/' - - -pathExists(path_resultsCLM) -pathExists(path_results) - - -limbs = [2490, 2500, 2510, 2540, 2570, 2571, 2573, 2574, 2590, 2600, 2601, 2610, 2620, 2631, 2640, 2642, 2650, 2651, 2652, 2653, 2654, 2655, 2660, - 2662, 2663, 2671, 2681, 2682, 2690, 2700, 2701, 2703, 2704, 2710, 2711, 2712, 2714, 2720, 2721, 2722, 2731, 2732, 2740, 2741, 2742, 2745, - 2746, 2750, 2751, 2752, 2754, 2755, 2760, 2761, 2762, 2771, 2772, 2780, 2790, 2831, 2840, 2850, 2870, 2880, 2881, 2882, 2890, 2901, 2902] -t = [249, 250, 251, 254, 257, 257, 257, 257, 259, 260, 260, 261, 262, 263, 264, 264, 265, 265, 265, 265, 265, 265, 266, 266, 266, 267, - 268, 268, 269, 270, 270, 270, 270, 271, 271, 271, 271, 272, 272, 272, 273, 273, 274, 274, 274, 274, 274, 275, 275, 275, 275, 275, 276, 276, 276, - 277, 277, 278, 279, 283, 284, 285, 287, 288, 288, 288, 289, 290, 290] - -Treal = np.arange(t[0], t[-1]+1, dtype=int) -newTotLimbs = len(Treal) - -totlimbs = len(limbs) -print(totlimbs, 'limbs!! \n') - - -# matrix with all Clm of all limbs -allClmMatrix = np.zeros((totlimbs, radiusDiscretisation, - 2, lmax, lmax), dtype=np.float32, order='C') - -pb = ProgressBar(0, totlimbs, c=5) # it should loop over totLimbs!! -printc('\n starting...', invert=1) -for j in pb.range(): - ############################################## - # loading voxel intensities - allIntensities = np.load(path + 'allIntensities_ReferenceShape_' + - str(limbs[j])[0:-1] + '_' + str(limbs[j])[-1] + '.npy') - allIntensitiesShape = allIntensities.shape - - ############################################## - # Forward Transformations (Splines and SPHARM) - Clm = forwardTransformation(allIntensities, N, lmax) - - allClmMatrix[j, :, :, :, :] = Clm - - del Clm, allIntensities - pb.print('Forward Transformations (splines and SPHARM) ...') - -np.save(path_resultsCLM + 'allClmMatrix', allClmMatrix) -# np.save(pathOutClm + 'samplePointsCoord', samplePointsCoord) -# np.save(pathOutClm + 'allIntensities', allIntensities) -np.save(path_resultsCLM+'allIntensitiesShape', allIntensitiesShape) -printc('\n allIntensitiesShape.npy \n', c='green') - - -############################################## -# splining -maxt = np.max(t) -mint = np.min(t) - -xnew = np.linspace(mint, maxt, newTotLimbs) -allClmSpline = np.zeros(shape=(newTotLimbs, radiusDiscretisation, - 2, allClmMatrix.shape[3], allClmMatrix.shape[4])) -# new clm from splines -range_m = np.linspace( - 0, newTotLimbs, num=allClmSpline.shape[0], endpoint=False).astype(int) - - -pb = ProgressBar(0, allClmMatrix.shape[1], c=5) -for f in pb.range(): - for ll in range(allClmMatrix.shape[2]): - for k in range(allClmMatrix.shape[3]): - for j in range(allClmMatrix.shape[4]): - spl = np.poly1d(np.polyfit(np.array(t), np.array( - allClmMatrix[:, f, ll, k, j]), deg_fit)) - ynew = spl(xnew) - - for m in range(allClmSpline.shape[0]): - allClmSpline[m, f, ll, k, j] = ynew[range_m[m]] - - pb.print('splining ...') - -print('allClmSpline.shape', allClmSpline.shape) - - -del allClmMatrix - - -np.save(path_resultsCLM + 'allClmSpline', allClmSpline) -printc('\n allClmSpline.npy \n', c='green') - - -############################################## -# vol parameters - -pathTmp = 'res/TIF-signedDist_sampleSize' + str(sampleSize) + '/' - - -volTmp = load(pathTmp + 'ReferenceShape_290_2.vti') -pos = volTmp.center() -rmax = volTmp.diagonalSize()/2 -volBounds = np.array(volTmp.GetBounds()) -np.save(path_resultsCLM + 'volBounds', volBounds) -printc('\n volBounds.npy saved\n', c='green') - -samplePoints = samplePoints(volTmp, expo, N, radiusDiscretisation) -del volTmp - -############################################## -# inverse Transformations -pb = ProgressBar(0, allClmSpline.shape[0], c=5) -for t in pb.range(): - ############################################## - # Inverse Transformations - ############################################## - inverse_Matrix = inverseTransformations( - allClmSpline[t, :, :, :, :], allIntensitiesShape, N, lmax) - - intensitiesreshape = np.reshape( - inverse_Matrix, inverse_Matrix.shape[0] * inverse_Matrix.shape[1]) - - del inverse_Matrix - - # ############################## - # # interpolateToImageData - voxBin = 100 # * radiusDiscretisation - apts = Points(samplePoints).addPointArray(intensitiesreshape, 'scals') - volume = interpolateToVolume(apts, kernel='shepard', radius=( - rmax / 20), dims=(voxBin, voxBin, voxBin), bounds=volBounds) - # printHistogram(volume, logscale=False, bins=25, c='g', minbin=3) - del apts - - ############################################## - # Reconstruction - write(volume, path_results + 'Limb-rec_' + - str(Treal[t]) + '.vti', binary=False) - write(volume.isosurface(threshold=-0.01).smoothWSinc(), - path_results + 'Limb-rec_' + str(Treal[t]) + '.vtk', binary=False) - - del volume - - pb.print('main reconstruction ... ') - - -############################################## diff --git a/Fearless/pureSPharm.py b/Fearless/pureSPharm.py deleted file mode 100644 index 4fce2dc..0000000 --- a/Fearless/pureSPharm.py +++ /dev/null @@ -1,211 +0,0 @@ -#!/usr/bin/env python -# -# @Author: Giovanni Dalmasso -# @Date: 15-Dec-2021 -# @Email: giovanni.dalmasso@embl.es -# @Project: FeARLesS -# @Filename: pureSPharm.py -# @Last modified by: gio -# @Last modified time: 02-May-2022 -# @License: MIT -# @Copyright: Copyright © 2021 Giovanni Dalmasso - - -from sys import argv, exit -from scipy.interpolate import griddata -import numpy as np - -from vedo import printc, load, spher2cart, mag, ProgressBar, Points, recoSurface, write -from utils import pathExists - -import pyshtools -############################################################# - - -def computeCLM(mesh, rmax, N, x0): - """Compute CLM.""" - # cast rays from the center and find intersections - agrid, pts = [], [] - for th in np.linspace(0, np.pi, N, endpoint=False): - lats = [] - for ph in np.linspace(0, 2*np.pi, N, endpoint=False): - p = spher2cart(rmax, th, ph) - intersections = mesh.intersectWithLine(x0, x0 + p) - if len(intersections): - value = mag(intersections[0]-x0) - lats.append(value) - pts.append(intersections[0]) - else: - lats.append(rmax) - # lats.append(0) - pts.append(p) - agrid.append(lats) - agrid = np.array(agrid) - - grid = pyshtools.SHGrid.from_array(agrid) - clm = grid.expand() - # grid_reco = clm.expand(lmax=lmax) # cut "high frequency" components - - return clm -############################################################# - - -##################################### -# PARAMETERS -parameters = argv -if len(parameters) != 2: - printc('missing parameters!!!', c='r') - exit() - -############################################################# -# maximum degree of the spherical harm. expansion -lmax = int(parameters[1]) -N = 500 # number of grid intervals on the unit sphere -rmax = 1400 -x0 = [0, 0, 0] # set object at this position -xLimb = [-200, 0, 200] -cutOrigin = [150, 0, 0] -deg_fit = 6 - - -DataPath = 'limbs-noFlank/' -path_results = 'res/' \ - 'pure_spharm' + '-lmax' + str(lmax) + '-N' + \ - str(N) + '-deg_fit' + str(deg_fit) + '/' - - -pathExists(path_results) - -printc('lmax =', lmax, 'N =', N, 'deg_fit =', deg_fit, c='y') - -printc("loading limbs ...", c='y') -limbs = load(DataPath + '*.vtk') - -totLimbs = len(limbs) -printc('tot # limbs --> ', totLimbs, c='y') - - -################################ -# finding time from limbs' file names -Tall = [] -for j in range(totLimbs): - Tall.append(float(limbs[j].filename.split('/')[-1].split('_')[1])) - -Tall = np.array(Tall) -printc('Tall \n', Tall, c='y') - -Treal = np.arange(Tall[0], Tall[-1]+1, dtype=int) - -NumRecLimbs = len(Treal) - - -Mclm = [] -pb = ProgressBar(0, totLimbs, c=2) -for j in pb.range(): - Mtmp = [] - clmAllTmp = [] - Mtmp.append(float(limbs[j].filename.split('/')[-1].split('_')[1])) - - clmTmp = computeCLM(limbs[j].pos(xLimb), rmax, N, x0) - - clmAllTmp.append(clmTmp.to_array()) - Mtmp.append(np.asarray(clmAllTmp)) - - Mclm.append(Mtmp) - - pb.print('clm...') - -CLM = sorted(Mclm, key=lambda tup: tup[0]) - -CLMtot = [] -for j in range(len(CLM)): - CLMtot.append(CLM[j][1]) - -CLMtot = np.asarray(CLMtot) -CLMtot = np.squeeze(CLMtot, axis=1) - -filename = 'clm_N' + str(N) + '_lmax'+str(lmax) + '.npy' -printc('saving --> ', filename, c='g') -np.save(path_results + filename, CLMtot) - - -# CLMtot = np.load(path_results + 'clm_N500_lmax50.npy') - -clmSpline = np.zeros( - shape=(NumRecLimbs, CLMtot.shape[1], CLMtot.shape[2], CLMtot.shape[3])) -print('clmSpline.shape', clmSpline.shape) - - -maxt = np.max(Treal) -mint = np.min(Treal) -xnew = np.linspace(mint, maxt, NumRecLimbs) -range_m = np.linspace( - 0, NumRecLimbs, num=clmSpline.shape[0], endpoint=False).astype(int) - - -pb = ProgressBar(0, CLMtot.shape[1], c=2) -for ll in pb.range(): - for k in range(CLMtot.shape[2]): - for j in range(CLMtot.shape[3]): - - spl = np.poly1d(np.polyfit( - np.array(Tall), np.array(CLMtot[:, ll, k, j]), deg_fit)) - ynew = spl(xnew) - - for m in range(clmSpline.shape[0]): - clmSpline[m, ll, k, j] = ynew[range_m[m]] - - pb.print('splines...') - - -pb = ProgressBar(0, clmSpline.shape[0], c=2) -for t in pb.range(): - - clmCoeffs = pyshtools.SHCoeffs.from_array(clmSpline[t]) - - grid_reco = clmCoeffs.expand(lmax=lmax) - # grid_reco.plot() - - ############################################## - agrid_reco = grid_reco.to_array() - - ll = [] - for i, long in enumerate(np.linspace(0, 360, num=agrid_reco.shape[1], endpoint=True)): - for j, lat in enumerate(np.linspace(90, -90, num=agrid_reco.shape[0], endpoint=True)): - th = np.deg2rad(90 - lat) - ph = np.deg2rad(long) - p = spher2cart(agrid_reco[j][i], th, ph) - ll.append((lat, long)) - - radii = agrid_reco.T.ravel() - n = 2*N * 1j - lnmin, lnmax = np.array(ll).min(axis=0), np.array(ll).max(axis=0) - grid = np.mgrid[lnmax[0]:lnmin[0]:n, lnmin[1]:lnmax[1]:n] - grid_x, grid_y = grid - agrid_reco_finer = griddata(ll, radii, (grid_x, grid_y), method='cubic') - - pts2 = [] - for i, long in enumerate(np.linspace(0, 360, num=agrid_reco_finer.shape[1], endpoint=False)): - for j, lat in enumerate(np.linspace(90, -90, num=agrid_reco_finer.shape[0], endpoint=True)): - th = np.deg2rad(90 - lat) - ph = np.deg2rad(long) - p = spher2cart(agrid_reco_finer[j][i], th, ph) - pts2.append(p) - - mesh2 = Points(pts2, r=20, c="r", alpha=1) - mesh2.clean(0.005) - - surfTmp = recoSurface(mesh2.cutWithPlane(origin=[-30, 0, 0]), - dims=100 - ) - - surf = surfTmp.extractLargestRegion().clone() - surf.smooth() - - # #Reconstruction - write(mesh2, path_results + 'Points_Limb-rec_' + - str(Treal[t]) + '.vtk', binary=False) - write(surf, path_results + 'Limb-rec_' + - str(Treal[t]) + '.vtk', binary=False) - - pb.print('rec ...') diff --git a/Fearless/utils.py b/Fearless/utils.py deleted file mode 100644 index 36958fe..0000000 --- a/Fearless/utils.py +++ /dev/null @@ -1,180 +0,0 @@ -#!/usr/bin/env python -# -# @Author: Giovanni Dalmasso -# @Date: 15-Dec-2021 -# @Email: giovanni.dalmasso@embl.es -# @Project: FeARLesS -# @Filename: utils.py -# @Last modified by: gio -# @Last modified time: 15-Dec-2021 -# @License: MIT -# @Copyright: Copyright © 2021 Giovanni Dalmasso - -import pyshtools -import gc -import numpy as np -import os -from vedo import printc, spher2cart, probePoints -import shutil -from sys import exit - - -def confirm(message): - """ - Ask user to enter Y or N (case-insensitive). - - :return: True if the answer is Y. - :rtype: bool - """ - answer = "" - while answer not in ["y", "n"]: - answer = input(message).lower() - return answer == "y" - - -def pathExists(path): - if not os.path.exists(path): - os.mkdir(path) - printc("Directory ", path, " Created ", c='green') - else: - printc("Directory ", path, " already exists", c='red') - if confirm("Should I delete the folder and create a new one [Y/N]? "): - shutil.rmtree(path) - os.mkdir(path) - printc("Directory ", path, " Created ", c='green') - else: - exit() - - -def voxelIntensity(vol, expo, N, radiusDiscretisation): - """Compute voxel intensities.""" - pos = vol.center() - rmax = vol.diagonalSize()/2 - - scalars = [] - - for th in np.linspace(0, np.pi, N, endpoint=False): - for ph in np.linspace(0, 2*np.pi, N, endpoint=False): - - # compute sample points - p = spher2cart(rmax, th, ph) - samplePointsTmp = [] - # making discretization more dense away from the center - p_tmp = p / (radiusDiscretisation-1)**expo - for j in range(radiusDiscretisation): - SP = pos + p_tmp * (j**expo) - samplePointsTmp.append(SP) - - # compute intensities - pb = probePoints(vol, samplePointsTmp) - - del samplePointsTmp - - # making the intensities growing outside the volume according to the gradient - scalarsTmp = pb.getPointArray() - nonz = np.nonzero(scalarsTmp)[0] - if len(nonz) > 2: - lastNoZeroId = nonz[-1] # find the last value != 0 - secondlastNoZeroId = nonz[-2] - # find the last value != 0 - lastNoZero = scalarsTmp[lastNoZeroId] - secondlastNoZero = scalarsTmp[secondlastNoZeroId] - dx = lastNoZero - secondlastNoZero - - for i in range(lastNoZeroId+1, len(scalarsTmp)): - scalarsTmp[i] = scalarsTmp[i-1] + dx - scalars.append(scalarsTmp.tolist()) - - del pb, scalarsTmp - - del vol - gc.collect() - - # return allIntensitiesMatrix - return np.array(scalars).reshape((N * N, radiusDiscretisation)) - - -def forwardTransformation(matrixOfIntensities, N, lmax): - - ############################################## - - coeff = matrixOfIntensities - - ############################################## - # SPHARNM - allClm = np.zeros((matrixOfIntensities.shape[1], 2, lmax, lmax)) - for j in range(allClm.shape[0]): - formattedcoeff = np.reshape(coeff[:, j], (N, N)) - SH = pyshtools.SHGrid.from_array(formattedcoeff) - clm = SH.expand() - - allClm[j, :, :, :] = clm.to_array(lmax=lmax - 1) - - del formattedcoeff, clm, matrixOfIntensities - - return allClm - - -def inverseTransformations(allClm, allIntensitiesShape, N, lmax): - """Make inverse SPHARM.""" - from scipy.interpolate import griddata - - aSH_recoMatrix = np.zeros((allIntensitiesShape[0], allIntensitiesShape[1])) - - for j in range(allClm.shape[0]): - # inverse SPHARM coefficients - clmCoeffs = pyshtools.SHCoeffs.from_array(allClm[j, :, :, :]) - SH_reco = clmCoeffs.expand(lmax=lmax - 1) - # grid_reco.plot() - aSH_reco = SH_reco.to_array() - - ############################## - pts1 = [] - ll = [] - for ii, long in enumerate(np.linspace(0, 360, num=aSH_reco.shape[1], endpoint=True)): - for jj, lat in enumerate(np.linspace(90, -90, num=aSH_reco.shape[0], endpoint=True)): - th = np.deg2rad(90 - lat) - ph = np.deg2rad(long) - p = spher2cart(aSH_reco[jj][ii], th, ph) - pts1.append(p) - ll.append((lat, long)) - - radii = aSH_reco.T.ravel() - - # make a finer grid - n = N * 1j - l_min, l_max = np.array(ll).min(axis=0), np.array(ll).max(axis=0) - grid = np.mgrid[l_max[0]:l_min[0]:n, l_min[1]:l_max[1]:n] - grid_x, grid_y = grid - agrid_reco_finer = griddata(ll, radii, (grid_x, grid_y), method='cubic') - ############################## - - formatted_aSH_reco = np.reshape(agrid_reco_finer, (N * N)) - - aSH_recoMatrix[:, j] = formatted_aSH_reco - - del formatted_aSH_reco, agrid_reco_finer, grid_x, grid_y, grid - - return aSH_recoMatrix - - -def samplePoints(vol, expo, N, radiusDiscretisation): - """Compute sample points.""" - pos = vol.center() - rmax = vol.diagonalSize()/2 - - samplePoints = [] - for th in np.linspace(0, np.pi, N, endpoint=False): - for ph in np.linspace(0, 2*np.pi, N, endpoint=False): - - # compute sample points - p = spher2cart(rmax, th, ph) - # making discretization more dense away from the center - p_tmp = p / (radiusDiscretisation-1)**expo - for j in range(radiusDiscretisation): - SP = pos + p_tmp * (j**expo) - samplePoints.append(SP) - - del vol - - return np.array(samplePoints) diff --git a/FearlessHearts b/FearlessHearts deleted file mode 160000 index b795abc..0000000 --- a/FearlessHearts +++ /dev/null @@ -1 +0,0 @@ -Subproject commit b795abc6d2176ee689d00dcfcf3d8438b23eb488 diff --git a/LICENSE b/LICENSE deleted file mode 100644 index 7162087..0000000 --- a/LICENSE +++ /dev/null @@ -1,21 +0,0 @@ -MIT License - -Copyright (c) 2021 Giovanni Dalmasso - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in all -copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE -SOFTWARE. diff --git a/README.md b/README.md deleted file mode 100644 index 085b0f2..0000000 --- a/README.md +++ /dev/null @@ -1,149 +0,0 @@ - -[![Contributors][contributors-shield]][contributors-url] -[![Forks][forks-shield]][forks-url] -[![Stargazers][stars-shield]][stars-url] -[![Issues][issues-shield]][issues-url] -[![MIT License][license-shield]][license-url] -[![CI status][CI-shield]][CI-url] - - - -

4D reconstruction of developmental trajectories
- using spherical harmonics

-

- - Twitter: giodalmasso - -

- - -### 🏠 [Homepage](https://vedo.embl.es/fearless/#/home) - -
- -

-Computer based approach to recreate the continuous evolution in time and space of developmental stages from 3D volumetric images. This method uses the mathematical approach of spherical harmonics to re-map discrete shape data into a space in which facilitates a smooth interpolation over time. - -This aproach was tested on mouse limb buds (from E10 to E12.5) and embryonic hearts (from 10 to 29 somites). - -A key advantage of this method is that the resulting 4D trajectory takes advantage of all the available data, while also being able to interpolate well through time intervals for which there is little or no data. - -This method/code can be used to recreate the 4D growth of embryonic organs from 3D image datasets of the paper: -Dalmasso _et al._, 4D reconstruction of murine developmental trajectories using spherical harmonics, Developmental -Cell (2022) --> https://doi.org/10.1016/j.devcel.2022.08.005 -

- - -
- -![video](https://user-images.githubusercontent.com/29924733/146750585-d6c0b9cb-8b5c-49c7-86f9-92fba875b14d.mp4) - - ---- -

- -## Datasets - - -All the data can be dowloaded from --> https://www.ebi.ac.uk/biostudies/studies/S-BIAD441 (folders `/limbs-noFlank/` and `/limbs+flank/`). - - -## Pipeline - -Follow the pipeline steps below to reproduce the analysis results. - - -#### `python pureSPharm.py` -- _Description:_ compute the spherical harmonics decomposition and reconstruction producing the 4D trajectory of the growing limb buds _without the flank_ (original data can be found in the folder `/limbs-noFlank/` of the archive). -- _Usage:_ in the code, `DataPath` should be change to the location of the folder `/limbs-noFlank/` downloaded from the archive. Run the code with the command: `python pureSPharm.py lmax`, where `lmax` is the desired degree of shaprical harmonics expansion. -- _Results:_ the results will be stored in a floder created automatically of the form `res/pure_spharm-lmax-N-deg_fit/` where `N` is the number of grid intervals on the sphere and `deg_fit` the degree of interpolation of the spherical harmonics coefficients. If the results folder already exists the code will ask if the user wants to delete it and continue or stop. - ---- - -#### `python makeVoxel.py` -- _Description:_ convert a vtk mesh from the limb-data files into voxel data (original data can be found in the folder `/limbs+flank/` of the archive). -- _Usage:_ in the code, `DataPath` should be change to the location of the folder `/limbs+flank/` downloaded from the archive. Run the code with the command: `python makeVoxel.py`. -- _Results:_ ihe results will be stored in a floder created automatically of the form `res/TIF-signedDist_sampleSize100/`. Changing in the code the variable `sampleSize` will also change the name of the results folder. If the results folder already exists the code will ask if the user wants to delete it and continue or stop. - ---- - -#### `python computeAllIntesities.py` -- _Description:_ compute the voxel intensities along the radii of a sphere of the voxel-limb-data obtained in the previous step. -- _Usage:_ in the code, `DataPath` should be change to the location of the folder `res/TIF-signedDist_sampleSize100/` obtained in the previous step. Run the code with the command: `python computeAllIntesities.py`. -- _Results:_ ihe results will be stored in a floder created automatically of the form `res/allIntensities-sampleSize100-radiusDiscretisation-N/` where `radiusDiscretisation` is the discretisation of the radii of the sphere and `N` is the number of grid intervals on the sphere. Changing in the code the variable `radiusDiscretisation` and `N` will also change the name of the results folder. If the results folder already exists the code will ask if the user wants to delete it and continue or stop. The results will be in the form of _numpy_ files, one for each limb. - ---- - -#### `python morphing.py` -- _Description:_ produce the 4D trajectory of the growing limb buds _with the flank_ using the voxel intensities computed in the previous step. -- _Usage:_ in the code, `path` should be change to the location of the folder `res/allIntensities-sampleSize100-radiusDiscretisation-N/`obtained in the previous step. Run the code with the command: `python morphing.py`. -- _Results:_ two folder will be created automatically, `res/CLM/morphing_sampleSize-radDisc-N-degFit-lmax/` and `res/morphing_sampleSize-radDisc-N-degFit-lmax/` (where `sampleSize` is voxel dimension of the data, `radDisc` is the discretisation of the radii of the sphere and `N` is the number of grid intervals on the sphere, `degFit` is the degree of interpolation of the spherical harmonics coefficients and `lmax` is the desired degree of shaprical harmonics expansion). In the first one, a matrix containing the shperical harmonics coefficients will be stored (in the form of _numpy_ file) and in the second the volumes and isosurfaces of the limbs forming the 4D trajectory. If the results folders already exist the code will ask if the user wants to delete them and continue or stop. - ---- - -#### `python utils.py` -- _Description:_ contains some basic functions used. - -

- ---- - -## Authors - -👤 **Giovanni Dalmasso** - -* Website: https://tinyurl.com/yc6pbyb2 -* Twitter: [@giodalmasso](https://twitter.com/giodalmasso) -* Github: [@gioda](https://github.com/gioda) -* LinkedIn: [@giovanni-dalmasso](https://linkedin.com/in/giovanni-dalmasso) - -👤 **Marco Musy** - -* Website: https://tinyurl.com/3zy9zmmy -* Github: [@marcomusy](https://github.com/marcomusy) - - -## 🤝 Contributing - -Contributions, issues and feature requests are welcome!
Feel free to check [issues page](https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/issues). - -## Show your support - -Give a ⭐️ if this project helped you!
- -Cite the code: [![DOI](https://zenodo.org/badge/434319643.svg)](https://zenodo.org/badge/latestdoi/434319643) -
- - -[![vedo_powered](https://user-images.githubusercontent.com/32848391/94372929-13e0e400-0102-11eb-938c-bc0274d57108.png)](https://github.com/marcomusy/vedo) - -![embl](https://user-images.githubusercontent.com/32848391/94371851-c3658880-00f9-11eb-9c2a-d418adb93d59.gif) - -## 📝 License - -Copyright © 2021 [Giovanni Dalmasso](https://github.com/gioda).
-This project is [MIT](https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/blob/main/LICENSE) licensed. - - - - - - - -[contributors-shield]: https://img.shields.io/github/contributors/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics -[contributors-url]: https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/graphs/contributors -[forks-shield]: https://img.shields.io/github/forks/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics -[forks-url]: https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/network/members -[stars-shield]: https://img.shields.io/github/stars/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics -[stars-url]: https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/stargazers -[issues-shield]: https://img.shields.io/github/issues/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics -[issues-url]: https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/issues -[license-shield]: https://img.shields.io/github/license/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics -[license-url]: https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/blob/master/LICENSE.txt -[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555 -[linkedin-url]: https://linkedin.com/in/giovanni-dalmasso -[product-screenshot]: images/screenshot.png - -[CI-shield]: https://github.com/dguo/make-a-readme/workflows/CI/badge.svg -[CI-url]: https://github.com/gioda/4D-reconstruction-of-developmental-trajectories-using-spherical-harmonics/actions - diff --git a/webpage/index.html b/webpage/index.html deleted file mode 100644 index 4ce4682..0000000 --- a/webpage/index.html +++ /dev/null @@ -1,298 +0,0 @@ - - - - - - Fearless Project - - - - - - - - - - - - - - - - -
- -
-
    -
    - - - -
    - - -
    -
    -

    Giovanni Dalmasso et al.

    -

    * * *

    -

    Fearless

    -

    4D reconstruction of developmental
    trajectories using spherical harmonics

    - -
    - - - - - - - - - - -
    - - - - - Map - - - - - -
    - - -
    -
    - - - - - -
    -
    - - - - -
    - -
    -

    Time sequence without the flank region

    -
    - -
    -
    -
    [hit arrow down for an interactive view..]
    -
    - -
    -
    -
    - Stage -
    -
    - -
    -
    - - - -
    -
    - -
    - [zoom & drag me - I'm 3D interactive!] -
    -
    - |Mouse --> Left-click: rotate scene, Shift-click: pan scene, Scroll: zoom scene in or out, Cntrl-click: rotate scene| -
    -
    - (Check out full documentation at: vedo.embl.es) -
    -
    - -
    - -
    - -
    -

    Time sequence with the flank region

    -
    - -
    -
    -
    [hit arrow down for an interactive view..]
    -
    - -
    -
    -
    - Stage -
    -
    - -
    -
    - - - -
    -
    - -
    - [zoom & drag me - I'm 3D interactive!] -
    -
    - |Mouse --> Left-click: rotate scene, Shift-click: pan scene, Scroll: zoom scene in or out, Cntrl-click: rotate scene| -
    -
    - (Check out full documentation at: vedo.embl.es) -
    -
    - -
    - -
    - -
    -

    Wildtype mouse heart growth

    -
    - -
    -
    -
    [hit arrow down for an interactive view..]
    -
    - - - - -
    -
    -
    - Stage -
    -
    - -
    -
    - - - -
    -
    - -
    - [zoom & drag me - I'm 3D interactive!] -
    -
    - |Mouse --> Left-click: rotate scene, Shift-click: pan scene, Scroll: zoom scene in or out, Cntrl-click: rotate scene| -
    -
    - (Check out full documentation at: vedo.embl.es) -
    - -
    [hit arrow down for more info...]
    -
    - - -
    -

    Wildtype mouse heart growth

    - - -
    - -
    - -
    - -
    - - - - - - - - - - - - - - - - - - -