Amend course schedule

NEUBIAS · Jul 8, 2024 · 682c867 · 682c867
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Showing 3 changed files with 11 additions and 7 deletions.
diff --git a/_includes/binarization/binarization_act1_skimage_napari.py b/_includes/binarization/binarization_act1_skimage_napari.py
@@ -2,13 +2,13 @@
 # Thresholding bright and dim cells
 
 # %%
-# Instantiate the napari
+# Instantiate napari
 import napari
-from OpenIJTIFF import open_ij_tiff
 viewer = napari.Viewer()
 
 # %%
 # Load the image
+from OpenIJTIFF import open_ij_tiff
 image, *_ = open_ij_tiff('https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_8bit__two_cells.tif')
 
 # %%
@@ -35,11 +35,11 @@
 
 # %%
 # Overlay the binary image
-viewer.add_image(binary_image_two_cells, opacity=0.8)
+viewer.add_labels(binary_image_two_cells, opacity=0.8)
 
 # %%
 # Apply a higher threshold
 # to only select the brighter cell
 # and also add this to the viewer
 binary_image_one_cell = image > 100
-viewer.add_image(binary_image_one_cell, opacity=0.8)
+viewer.add_labels(binary_image_one_cell, opacity=0.8)
diff --git a/_includes/measure_shapes/measure_shapes_act1.md b/_includes/measure_shapes/measure_shapes_act1.md
@@ -1,4 +1,4 @@
-<h4 id='measure_act1'><a href="#measure_act1">Measure object shapes in a digital image</a></h4>
+<h4 id='measure_2d_shapes'><a href="#measure_2d_shapes">Measure 2-D shapes in an image</a></h4>
 
 - Using a drawing board, discuss important shape features and concepts, such as,
   - Area
@@ -14,7 +14,7 @@
 - Discuss how objects can be distiguished by various shape measurements
 - Perform shape measurements in pixel or calibrated units
 
-### Example data
+##### Example data
 
 - Fluorescence image with nuclei of different shapes: [xy_16bit_calibrated__nuclei_various_shapes.tif](https://github.com/NEUBIAS/training-resources/raw/master/image_data/xy_16bit_calibrated__nuclei_various_shapes.tif)
   - Useful for manual delineation of objects and subsequent measurements

diff --git a/courses/2024_07_IDIP-Heidelberg_skimage_napari_beginners.md b/courses/2024_07_IDIP-Heidelberg_skimage_napari_beginners.md
@@ -87,9 +87,13 @@ The first day is an onboarding day to bring everyone to the same level on basic
     - [Max and sum projections of an anisotropic image]()
 
 ### Image analysis basics (day 2)
-
 1. [Segmentation](https://neubias.github.io/training-resources/segmentation/index.html)
     - Arif Khan
+1. [Workflow: Basic 2D object analysis](https://neubias.github.io/training-resources/workflow_segment_2d_nuc    lei_measure_shape/index.html)
+    - Arif Khan
+    - Only discuss the figure:
+        - The most basic segmentation workflow
+        - The components of this workflow will be taught now
 1. [Manual thresholding](https://neubias.github.io/training-resources/binarization/index.html)
     - Arif Khan
 1. [Automated thresholding](https://neubias.github.io/training-resources/auto_threshold/index.html)