.flake8
.gitignore
.pre-commit-config.yaml
.readthedocs.yaml
LICENSE
MANIFEST.in
README.md
coverage-check.sh
coverage.xml
pypi-README.md
pyproject.toml
requirements.txt
setup.py
.github/workflows/workflow.yml
conda/eggplant.yaml
data-processing/human-breast-cancer/download-data.sh
data-processing/human-breast-cancer/make-h5ad.py
data-processing/human-developmental-heart/download-data.sh
data-processing/human-developmental-heart/make-h5ad.py
data-processing/mob/download-data.sh
data-processing/mob/make-h5ad.py
data-processing/mouse-hippocampus/download-data.sh
data-processing/mouse-hippocampus/make-h5ad.py
data/human-breast-cancer/landmarks/bcA.tsv
data/human-breast-cancer/landmarks/bcB.tsv
data/human-breast-cancer/sterescope/bcA.tsv
data/human-breast-cancer/sterescope/bcB.tsv
data/human-developmental-heart/landmarks/V10B01-014_A1.tsv
data/human-developmental-heart/landmarks/V10F24-105_A1.tsv
data/human-developmental-heart/landmarks/V10F24-105_B1.tsv
data/human-developmental-heart/landmarks/V10F24-105_C1.tsv
data/human-developmental-heart/landmarks/V10F24-105_D1.tsv
data/human-developmental-heart/landmarks/V10S28-368_D1.tsv
data/human-developmental-heart/landmarks/V10S28-371_A1.tsv
data/human-developmental-heart/references/landmarks.tsv
data/human-developmental-heart/references/reference.png
data/mob/landmarks/Rep10_MOB.tsv
data/mob/landmarks/Rep11_MOB.tsv
data/mob/landmarks/Rep12_MOB.tsv
data/mob/landmarks/Rep1_MOB.tsv
data/mob/landmarks/Rep2_MOB.tsv
data/mob/landmarks/Rep3_MOB.tsv
data/mob/landmarks/Rep4_MOB.tsv
data/mob/landmarks/Rep5_MOB.tsv
data/mob/landmarks/Rep6_MOB.tsv
data/mob/landmarks/Rep7_MOB.tsv
data/mob/landmarks/Rep8_MOB.tsv
data/mob/landmarks/Rep9_MOB.tsv
data/mob/references/landmarks.tsv
data/mob/references/reference.png
data/mouse-hippocampus/landmarks/hippo-slide_seq.tsv
data/mouse-hippocampus/landmarks/hippo-visium.tsv
data/mouse-hippocampus/references/landmarks.tsv
data/mouse-hippocampus/references/reference.png
data/synthetic/references/landmarks.tsv
data/synthetic/references/reference.png
data/synthetic/templates/imgs/reference.png
data/synthetic/templates/imgs/t_0.png
data/synthetic/templates/imgs/t_1.png
data/synthetic/templates/imgs/t_2.png
data/synthetic/templates/imgs/t_3.png
data/synthetic/templates/imgs/t_4.png
data/synthetic/templates/imgs/t_5.png
data/synthetic/templates/imgs/t_6.png
data/synthetic/templates/imgs/t_7.png
data/synthetic/templates/landmarks/reference_landmarks.tsv
data/synthetic/templates/landmarks/t_0_landmarks.tsv
data/synthetic/templates/landmarks/t_1_landmarks.tsv
data/synthetic/templates/landmarks/t_2_landmarks.tsv
data/synthetic/templates/landmarks/t_3_landmarks.tsv
data/synthetic/templates/landmarks/t_4_landmarks.tsv
data/synthetic/templates/landmarks/t_5_landmarks.tsv
data/synthetic/templates/landmarks/t_6_landmarks.tsv
data/synthetic/templates/landmarks/t_7_landmarks.tsv
docs/Makefile
docs/make.bat
docs/requirements.txt
docs/source/about.rst
docs/source/conf.py
docs/source/eggplant.rst
docs/source/glossary.rst
docs/source/index.rst
docs/source/install.rst
docs/source/modules.rst
docs/source/ref.bib
docs/source/tutorials.rst
docs/source/_static/css/custom.css
docs/source/auto/ref.el
docs/source/images/flow.png
docs/source/images/flow.svg
docs/source/images/fullflow.png
docs/source/images/logo.png
docs/source/notebooks/estimate-number-of-landmarks.ipynb
docs/source/notebooks/mouse-olfactory-bulb-analysis.ipynb
docs/source/notebooks/spatiotemporal.ipynb
eggplant/__init__.py
eggplant/constants.py
eggplant/methods.py
eggplant/models.py
eggplant/ode.py
eggplant/plot.py
eggplant/preprocess.py
eggplant/sdea.py
eggplant/utils.py
image-processing/compile-horizontal-figure.py
images/bugcatcher.png
images/innovator.jpg
images/logo.png
landmark-selection/chart.py
landmark-selection/tmp
notebooks/MOB.ipynb
notebooks/estimate-number-of-landmarks.ipynb
notebooks/human-breast-cancer.ipynb
notebooks/human-developmental-heart.ipynb
notebooks/mouse-hippocampus.ipynb
notebooks/n_components.ipynb
notebooks/show-references.ipynb
notebooks/skip.VI-MOB.ipynb
notebooks/skip.autoencoder.ipynb
notebooks/skip.compare-fa-vs-normal.ipynb
notebooks/skip.fa-MOB-play.ipynb
notebooks/skip.fa-vs-exact.ipynb
notebooks/synthetic-1-generation-and-analysis.ipynb
notebooks/synthetic-2-generation-and-analysis.ipynb
notebooks/.ipynb_checkpoints/ode-movement-checkpoint.ipynb
spatial_eggplant.egg-info/PKG-INFO
spatial_eggplant.egg-info/SOURCES.txt
spatial_eggplant.egg-info/dependency_links.txt
spatial_eggplant.egg-info/requires.txt
spatial_eggplant.egg-info/top_level.txt
test/__init__.py
test/test_methods.py
test/test_model.py
test/test_plot.py
test/test_preprocess.py
test/test_sdea.py
test/test_utils.py
test/utils.py