Add JUMP image data compatibility and example notebook (#18)

* add testing data

* add additional orig images

* add exception messages for #15

* add imagecodecs; jupyterlab deps

* shift to mask focus for current outlines

* update to outline method; tests; outline image nms

* add docs; slight modifications; example notebook

* linting

docs/src/examples.md

@@ -0,0 +1,10 @@
+# Examples
+
+```{toctree}
+---
+caption: "List of examples"
+maxdepth: 2
+glob:
+---
+examples/*
+```

docs/src/examples/cytodataframe_at_a_glance.py

@@ -0,0 +1,109 @@
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.16.4
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# # CytoDataFrame at a Glance
+#
+# This notebook demonstrates various capabilities of
+# [CytoDataFrame](https://github.com/WayScience/CytoDataFrame) using examples.
+#
+# CytoDataFrame is intended to provide you a Pandas-like
+# DataFrame experience which is enhanced with single-cell
+# visual information which can be viewed directly in a Jupyter notebook.
+
+# +
+from cytodataframe.frame import CytoDataFrame
+
+# create paths for use with CytoDataFrames below
+jump_data_path = "../../../tests/data/cytotable/JUMP_plate_BR00117006"
+nf1_cellpainting_path = "../../../tests/data/cytotable/NF1_cellpainting_data_shrunken/"
+nuclear_speckles_path = "../../../tests/data/cytotable/nuclear_speckles"
+# -
+# %%time
+# view JUMP plate BR00117006 with images
+CytoDataFrame(
+    data=f"{jump_data_path}/BR00117006_shrunken.parquet",
+    data_context_dir=f"{jump_data_path}/images/orig",
+)[
+    [
+        "Metadata_ImageNumber",
+        "Cells_Number_Object_Number",
+        "Image_FileName_OrigAGP",
+        "Image_FileName_OrigDNA",
+        "Image_FileName_OrigRNA",
+    ]
+][:3]
+
+# %%time
+# view JUMP plate BR00117006 with images and overlaid outlines for segmentation
+CytoDataFrame(
+    data=f"{jump_data_path}/BR00117006_shrunken.parquet",
+    data_context_dir=f"{jump_data_path}/images/orig",
+    data_outline_context_dir=f"{jump_data_path}/images/outlines",
+)[
+    [
+        "Metadata_ImageNumber",
+        "Cells_Number_Object_Number",
+        "Image_FileName_OrigAGP",
+        "Image_FileName_OrigDNA",
+        "Image_FileName_OrigRNA",
+    ]
+][:3]
+
+
+# %%time
+# view NF1 Cell Painting data with images
+CytoDataFrame(
+    data=f"{nf1_cellpainting_path}/Plate_2_with_image_data_shrunken.parquet",
+    data_context_dir=f"{nf1_cellpainting_path}/Plate_2_images",
+)[
+    [
+        "Metadata_ImageNumber",
+        "Metadata_Cells_Number_Object_Number",
+        "Image_FileName_GFP",
+        "Image_FileName_RFP",
+        "Image_FileName_DAPI",
+    ]
+][:3]
+
+# %%time
+# view NF1 Cell Painting data with images and overlaid outlines from masks
+CytoDataFrame(
+    data=f"{nf1_cellpainting_path}/Plate_2_with_image_data_shrunken.parquet",
+    data_context_dir=f"{nf1_cellpainting_path}/Plate_2_images",
+    data_mask_context_dir=f"{nf1_cellpainting_path}/Plate_2_masks",
+)[
+    [
+        "Metadata_ImageNumber",
+        "Metadata_Cells_Number_Object_Number",
+        "Image_FileName_GFP",
+        "Image_FileName_RFP",
+        "Image_FileName_DAPI",
+    ]
+][:3]
+
+# %%time
+# view nuclear speckles data with images and overlaid outlines from masks
+CytoDataFrame(
+    data=f"{nuclear_speckles_path}/test_slide1_converted.parquet",
+    data_context_dir=f"{nuclear_speckles_path}/images/plate1",
+    data_mask_context_dir=f"{nuclear_speckles_path}/masks/plate1",
+)[
+    [
+        "Metadata_ImageNumber",
+        "Nuclei_Number_Object_Number",
+        "Image_FileName_A647",
+        "Image_FileName_DAPI",
+        "Image_FileName_GOLD",
+    ]
+][:3]

docs/src/index.md

@@ -12,6 +12,7 @@ relative-images:
 caption: 'Contents:'
 maxdepth: 3
 ---
+examples
 python-api
 presentations
 contributing