Extract all images and add to lancedb

.gitignore

@@ -22,3 +22,7 @@ __pycache__/
 # data packaging ignores
 5.data_packaging/packaged
 5.data_packaging/images
+
+*.txt
+*.csv
+*.parquet

5.data_packaging/example.py

@@ -0,0 +1,42 @@
+# ---
+# jupyter:
+#   jupytext:
+#     text_representation:
+#       extension: .py
+#       format_name: light
+#       format_version: '1.5'
+#       jupytext_version: 1.18.1
+#   kernelspec:
+#     display_name: Python 3 (ipykernel)
+#     language: python
+#     name: python3
+# ---
+
+# # Example for using packaged data
+#
+# This notebook shows how to use the packaged data from this project.
+
+# +
+import lancedb
+from serpula_rasa.image import show_images_from_lance
+
+# setup a connection to lancedb
+ldb = lancedb.connect(uri=(lance_dir := "packaged/lancedb/mitocheck_data"))
+# -
+
+# show all table names
+# note: all table names include numbers corresponing to the step they came from.
+ldb.table_names(limit=20)
+
+ldb.open_table(name="5.data_packaging.location_and_ch5_frame_image_data").to_pandas().head()
+
+show_images_from_lance(
+    db_path=lance_dir,
+    table_name="5.data_packaging.location_and_ch5_frame_image_data",
+    col_name="ome-arrow_original",
+    max_images=20,
+    pick="first",
+    cmap="gray",
+    base_size=10,
+    cols=1,
+)