Implement 12 bit saturation activity for datatypes module

_includes/datatypes/inspect_12bit_saturation_skimage_napari.py

@@ -8,13 +8,16 @@
 import matplotlib.pyplot as plt
 from OpenIJTIFF import open_ij_tiff
 
-viewer = napari.Viewer()
-
 # %%
-# Open an image and view it
+# Open an image and view it in napari
 image, *_ = open_ij_tiff('https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_12bit__saturated_plant.tif')
+viewer = napari.Viewer()
 viewer.add_image(image)
 
+# %%
+# Napari:
+# - Hover with the mouse to look for saturation
+
 # %% 
 # Check the image's datatype
 print(image.dtype)
@@ -27,6 +30,21 @@
 # - Important algorithms, e.g. for spot detection, do not work well in regions with intensity clipping
 print("Min:", image.min()) # Are there any clipped pixels?
 print("Max:", image.max()) # Are there any clipped pixels?
-print("Number of 0 pixels:", np.sum(image==0)) # How many clipped pixels are there?
-print("Number of 255 pixels:", np.sum(image==255))
-plt.hist(image.flatten(), bins=np.arange(image.min(), image.max() + 1));
+
+# %% 
+# Compute the maximal value of various data types,
+# and observe that, suspiciously, our image's maximum value 
+# matches that of a 12-bit image
+print("8 bit max:", 2**8-1)
+print("12 bit max:", 2**12-1)
+print("16 bit max:", 2**16-1)
+
+# %% 
+# Check how many satured pixels we have
+print("Number of 4095 pixels:", np.sum(image==4095))
+
+# %%
+# To double check that this really is a 12 bit image 
+# you can try to inspect the image metadata
+# - If you open the image in Fiji you can do: Image > Show Info
+# - TODO: find out how to do this in python

_includes/datatypes/inspect_8bit_saturation_skimage_napari.py

@@ -31,4 +31,4 @@
 print("Max:", image.max()) # Are there any clipped pixels?
 print("Number of 0 pixels:", np.sum(image==0)) # How many clipped pixels are there?
 print("Number of 255 pixels:", np.sum(image==255))
-plt.hist(image.flatten(), bins=np.arange(image.min(), image.max() + 1));
+plt.hist(image.flatten(), bins=np.arange(image.min(), image.max() + 1));

courses/2024_07_IDIP-Heidelberg_skimage_napari_beginners.md

@@ -73,6 +73,8 @@ The first day is an onboarding day to bring everyone to the same level on basic
     - Felix Schneider
 1. [Spatial image calibration](https://neubias.github.io/training-resources/spatial_calibration/index.html) 
     - Christian Tischer
+    - [8 bit saturation]()
+    - [12 bit saturation]()
 1. [N-dimensional images](https://neubias.github.io/training-resources/multidimensional_image_basics/index.html)
     - Arif Khan
 1. [Image data types](https://neubias.github.io/training-resources/datatypes/index.html)