initial documentation update

MannLabs · May 30, 2024 · 841cd55 · 841cd55
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diff --git a/docs/html/_images/sparcspy_workflow_steps_with_explaination 2.png b/docs/html/_images/sparcspy_workflow_steps_with_explaination 2.png
diff --git a/docs/html/_images/sparcspy_workflow_steps_with_explaination.pdf b/docs/html/_images/sparcspy_workflow_steps_with_explaination.pdf
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
@@ -1,4 +1,4 @@
-SPARCSpy - image-based single cell analysis at scale in python
+SPARCSpy - image-based single cell analysis at scale in Python
 ===============================================================
 
 SPARCSpy is a scalable toolkit to analyse single-cell image datasets. This Python implementation efficiently segments individual cells, generates single-cell datasets and provides tools for the efficient deep learning classification of their phenotypes for downstream applications.

diff --git a/docs/html/_sources/pages/example_notebooks.rst.txt b/docs/html/_sources/pages/example_notebooks.rst.txt
@@ -0,0 +1,32 @@
+Example Notebooks
+=====================
+
+Basic SPARCSpy Project
+----------------------
+
+This notebook demonstrates the basic functionality of SPARCSpy. It shows you how to initialize a SPARCSpy project, load input images, segment, extract and classify the provided data and how to generate cutting instructions for excision on a leica LMD7 microscope.
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/example_sparcspy_project.ipynb
+
+Timecourse SPARCSpy Project
+---------------------------
+
+This notebook demonstrates how to use SPARCSpy to analyze a timecourse experiment. It shows you how to initialize a SPARCSpy project, load input images, segment, extract and classify the provided data and how to generate cutting instructions for excision on a leica LMD7 microscope.
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/Example_Notebook_TimeCourse_Project.ipynb
+
+Segmentation Workflows
+----------------------
+
+This notebook walks you through the currently implemented segmentation workflows.
+
+.. toctree::
+   :maxdepth: 2
+
+   notebooks/example_notebook_segmentation_workflows.ipynb
diff --git a/docs/html/_sources/pages/module/ml.rst.txt b/docs/html/_sources/pages/module/ml.rst.txt
@@ -0,0 +1,59 @@
+*******************
+ml
+*******************
+
+.. toctree::
+   :maxdepth: 3
+
+datasets
+########
+
+.. automodule:: sparcscore.ml.datasets
+    :members:
+
+metrics
+########
+
+.. automodule:: sparcscore.ml.metrics
+    :members:
+
+models
+########
+
+.. autoclass:: sparcscore.ml.models.VGGBase
+    :members:
+    :show-inheritance: False
+
+.. autoclass:: sparcscore.ml.models.VGG1
+    :members:
+    :show-inheritance:
+
+.. autoclass:: sparcscore.ml.models.VGG2
+    :members:
+    :show-inheritance:
+
+
+plmodels
+########
+
+.. autoclass:: sparcscore.ml.plmodels.MultilabelSupervisedModel
+    :members:
+    :show-inheritance: False
+
+pretrained_models
+#################
+
+.. automodule:: sparcscore.ml.pretrained_models
+    :members:
+
+transforms
+###########
+
+.. automodule:: sparcscore.ml.transforms
+    :members:
+
+utils
+###########
+
+.. automodule:: sparcscore.ml.utils
+    :members:
diff --git a/docs/html/_sources/pages/module/processing.rst.txt b/docs/html/_sources/pages/module/processing.rst.txt
@@ -0,0 +1,18 @@
+*******************
+processing
+*******************
+
+utils
+######
+.. automodule:: sparcscore.processing.utils
+    :members:
+
+preprocessing
+#############
+.. automodule:: sparcscore.processing.preprocessing
+    :members:
+
+segmentation
+############
+.. automodule:: sparcscore.processing.segmentation
+    :members: