Various updates to python activities on multiscale and spatial calibration

_includes/multidimensional_images/multidimensional_images_act1_skimage_napari.py

@@ -1,19 +1,22 @@
-# %% [markdown]
-# ## Explore a 3D image
+# %%
+# Explore a 3D image
 
 # %%
-# Load the image
+# Imports
 from OpenIJTIFF import open_ij_tiff
+from napari.viewer import Viewer
+
+# %%
+# Load the image
 image, axes, scales, units = open_ij_tiff("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyz_8bit__chromosomes.tif")
 
 # View the image in napari
-from napari.viewer import Viewer
 napari_viewer = Viewer()
 napari_viewer.add_image(image)
 
-# %% [markdown]
-# **Napari GUI** Explore different sliders and values in the bottom left part \
-# **Napari GUI** Show in 3D. Note that the scalings are not yet correct. 
+# [markdown]
+# Napari GUI: Explore different sliders and values in the bottom left part.
+# Napari GUI: Show in 3D. Note that the scalings are not yet correct.
 
 # %%
 # Print image axes metadata
@@ -23,8 +26,8 @@
 print("Units: ", units)
 
 # %%
-# Add image with scaling. 
-napari_viewer.add_image(image, name = "Scaled image", scale = scales) 
+# Add image with scaling.
+napari_viewer.add_image(image, name = "Scaled image", scale = scales)
 
-# %% [markdown]
-# **Napari GUI** View scaled image in 3D. Note that the scaling is now correct. 
+# %%
+# Napari GUI: View scaled image in 3D. Note that the scaling is now correct.

_includes/multidimensional_images/multidimensional_images_act2_skimage_napari.py

@@ -1,9 +1,13 @@
-# %% [markdown]
+# %%
 # ## Explore a 3D multi-channel image
 
 # %%
-# Load the image 
+# Imports
 from OpenIJTIFF import open_ij_tiff
+from napari.viewer import Viewer
+
+# %%
+# Load the image
 image, axes, scales, units = open_ij_tiff("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyzc_8bit_beads_p_open.tif")
 
 # %%
@@ -15,13 +19,12 @@
 
 # %%
 # View the image
-from napari.viewer import Viewer
 napari_viewer = Viewer()
 napari_viewer.add_image(image, scale = scales)
 
-# %% [markdown]
-# **Napari GUI** Explore different sliders and values in the bottom left part \
-# **Napari GUI** Delete the image
+# %%
+# Napari GUI: Explore different sliders and values in the bottom left part.
+# Napari GUI: Delete the image.
 
 # %%
 # Create images as separate channels
@@ -41,5 +44,5 @@
 napari_viewer.add_image(image_ch0, name = 'Ch0_ns', colormap = 'magenta')
 napari_viewer.add_image(image_ch1, name = 'Ch1_ns', colormap = 'green', blending='additive')
 
-# %% [markdown]
-# **Napari GUI** Explore different blending modes and LUTs
+# %%
+# Napari GUI: Explore different blending modes and LUTs.

_includes/multidimensional_images/multidimensional_images_act3_skimage_napari.py

@@ -1,9 +1,13 @@
-# %% [markdown]
-# ## Inspect a 3D time-lapse image
+# %%
+# Inspect a 3D time-lapse image
 
 # %%
-# Load the image
+# Imports
 from OpenIJTIFF import open_ij_tiff
+from napari.viewer import Viewer
+
+# %%
+# Load the image
 image, axes, scales, units = open_ij_tiff("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyzt_8bit__starfish_chromosomes.tif")
 
 # %%
@@ -15,10 +19,9 @@
 
 # %%
 # View the image
-from napari.viewer import Viewer
 napari_viewer = Viewer()
 napari_viewer.add_image(image, scale = scales)
 
-# %% [markdown]
-# **Napari GUI** Explore different axes sliders and values in the bottom left part \
-# **Napari GUI** Show in 3D. 
+# %%
+# Napari GUI: Explore different axes sliders and values in the bottom left part.
+# Napari GUI: Show in 3D.

_includes/multidimensional_images/multidimensional_images_act4_skimage_napari.py

@@ -1,9 +1,14 @@
-# %% [markdown]
-# ## Explore a 5D image (3D image + channels + time)
+# %%
+# Explore a 5D image (3D image + channels + time)
 
 # %%
-# Load the image
+# Imports
 from OpenIJTIFF import open_ij_tiff
+from napari.viewer import Viewer
+import numpy as np
+
+# %%
+# Load the image
 image, axes, scales, units = open_ij_tiff("https://github.com/NEUBIAS/training-resources/raw/master/image_data/xyzct_16bit__metaphase_eb3_cenpa.tif")
 
 # %%
@@ -15,14 +20,14 @@
 
 # %%
 # Display image in napari
-from napari.viewer import Viewer
 napari_viewer = Viewer()
 napari_viewer.add_image(image, scale = scales)
 
-# %% [markdown]
-# **Napari GUI** Explore different sliders and values in the bottom left part \
-# **Napari GUI** Show in 3D. Note that the order of axes is not yet correct.\ Napari expects that the last 3 dimension are ZYX\
-# **Napari GUI** Delete image 
+# %%
+# Napari GUI: Explore different sliders and values in the bottom left part.
+# Napari GUI: Show in 3D. Note that the order of axes is not yet correct.
+#             Napari expects that the last 3 dimension are ZYX.
+# Napari GUI: Delete image.
 
 # %%
 # Remove channel from scale
@@ -36,23 +41,22 @@
 napari_viewer.add_image(image[:,:,0,:,:], scale = scales_tzyx, name = 'Ch0', colormap = 'magenta')
 napari_viewer.add_image(image[:,:,1,:,:], scale = scales_tzyx, name = 'Ch1', colormap = 'green', blending='additive')
 
-# %% [markdown]
-# **Napari GUI** Explore different sliders and values in the bottom left part \
-# **Napari GUI** delete image and try direct loading
+# %%
+# Napari GUI: Explore different sliders and values in the bottom left part.
+# Napari GUI: delete image and try direct loading.
 
 # %%
 # View image as separate channels in one step
 napari_viewer.add_image(image, channel_axis = 2, scale = scales_tzyx, name = ['Ch0', 'Ch1'])
 
-# %% [markdown]
-# **Napari GUI** delete image 
+# %%
+# Napari GUI: delete image.
 
 # %%
 # Loading with numpy transpose
-import numpy as np
 image_transpose = np.transpose(image, (2, 0, 1, 3, 4))
 scales_transpose = [scales[2],scales[0],scales[1],scales[3],scales[4]]
 napari_viewer.add_image(image_transpose, scale = scales_transpose)
 
-# %% [markdown]
-# **Napari GUI** Right mouse click on image and `split stack`. This will generate visible two channels
+# %%
+# Napari GUI: Right mouse click on image and `split stack`. This will generate visible two channels.

_includes/spatial_calibration/spatial_calibration_act1_skimage_napari.py

@@ -1,7 +1,5 @@
-# %% [markdown]
-# ## Spatial image calibration
-# #### Requirements
-# - [skimage and napari](https://neubias.github.io/training-resources/tool_installation/index.html#skimage_napari)
+# %%
+# Spatial image calibration
 
 # %%
 # Import python packages.
@@ -27,15 +25,15 @@
 napari_viewer = Viewer()
 napari_viewer.add_image(image, scale=voxel_size)
 
-# %% [markdown]
-# **Napari GUI**: Change the axes order using the corresponding button. \
-# **Napari GUI**: Use the 3D viewer button to render the image in 3D.
+# %%
+# Napari GUI: Change the viewer dimension order using the corresponding button.
+# Napari GUI: Use the 3D viewer button to render the image in 3D.
 
-# %% [markdown]
-# ### Compute distances between points
+# %%
+# Compute distances between points
 #
-# **Napari GUI** use the `New points layer button` to create a new points layer \
-# **Napari GUI** use `Add points` to add two points somewhere on the meta-phase plate \
+# Napari GUI: use the `New points layer button` to create a new points layer.
+# Napari GUI: use `Add points` to add two points somewhere on the meta-phase plate.
 
 # %%
 # extract point coordinates
@@ -51,7 +49,7 @@
 print("Voxel size: ", voxel_size)
 
 # %%
-points_cal = points * scale 
+points_cal = points * scale
 print("Points :\n", points)
 print("Calibrated points :\n", points_cal)
 

_includes/spatial_calibration/spatial_calibration_act2_skimage_napari.py

@@ -1,14 +1,12 @@
-# %% [markdown]
-# ## Spatial image calibration
-# #### Requirements
-# - [skimage and napari](https://neubias.github.io/training-resources/tool_installation/index.html#skimage_napari)
+# %%
+# Spatial image calibration
 
 # %%
 # Import python packages.
 import os
 from OpenIJTIFF import open_ij_tiff, save_ij_tiff
-import numpy as np
 from napari.viewer import Viewer
+import numpy as np
 
 # %%
 # Open a 2D image and its axes metadata
@@ -39,9 +37,9 @@
 # %%
 # Note that the 3D image does not have calibrated metadata.
 # Let's add spatial calibration using the x&y voxel_size from the 2D image
-# and also add a z scaling 
+# and also add a z scaling
 voxel_size_image_3D = [0.52, voxel_size_image_2D[1], voxel_size_image_2D[0]]
-units_image_3D = ["um","um","um"]
+units_image_3D = ["um", "um", "um"]
 
 # %%
 # Inspect the metadata for the 3D image
@@ -51,13 +49,11 @@
 print("Units: ", units_image_3D)
 
 # %%
-# Open napari and add the images with their voxel sizes as scaling
+# Open napari and add the 3D image with voxel_size
 napari_viewer = Viewer()
-napari_viewer.add_image(image_2D, scale=voxel_size_image_2D, name='image_2D')
 napari_viewer.add_image(image_3D, scale=voxel_size_image_3D, name='image_3D')
 
-# %% [markdown]
-# Napari GUI: Change the axes order using the corresponding button. \
+# %%
 # Napari GUI: Use the 3D viewer button to render the image in 3D.
 
 # %%
@@ -73,3 +69,21 @@
 
 # %%
 # Open the above file in FIJI and verify image scales were properly saved.
+
+# %%
+# Measure the length of the nucleus (as exercise)
+# Napari GUI: use the `New points layer button` to create a new points layer.
+# Napari GUI: use `Add points` to add two points along the longest axis
+
+# %%
+# points = napari_viewer.layers['Points'].data
+# scale = napari_viewer.layers['Points'].scale
+# points_cal = points * scale
+# print("Points :\n", points)
+# print("Calibrated points :\n", points_cal)
+
+# %%
+# diff_vector = points_cal[1] - points_cal[0]
+# sqr_diff_vector = diff_vector ** 2
+# distance = np.sqrt(sqr_diff_vector.sum())
+# print('Distance:', distance)