Merge pull request NEUBIAS#600 from NEUBIAS/improve_spatial_calibrati…

…on_figure Improve spatial calibration figure and concept map
oanegros · Sep 25, 2023 · 89843e5 · 89843e5
2 parents 8599a36 + 908a0f9
commit 89843e5
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diff --git a/_includes/spatial_calibration/scale_bar.md b/_includes/spatial_calibration/scale_bar.md
@@ -1,4 +1,4 @@
-<h4 id='scale_bar'><a href="#scale_bar>Inspect spatial calibration metadata and add a scale bar</a></h4>
+<h4 id='scale_bar'><a href="#scale_bar">Inspect spatial calibration metadata and add a scale bar</a></h4>
   - Open an image and inspect the spatial calibration metadata 
   - Add a scale bar to the image  
 

diff --git a/_modules/spatial_calibration.md b/_modules/spatial_calibration.md
@@ -19,13 +19,12 @@ motivation: >
 
 concept_map: >
   graph TD
-    Im("Image") -->|has many| P("Pixel/Voxel")
-    Im --> |has| C("Calibration")
-    P -->|has| Va("Value")
-    P -->|has| I("Indices")
-    P --> |has| RWC("Real world coordinate")
-    C --> RWC
-    I --> RWC
+    Im("Image") --> P("Pixels")
+    Im --> C("Calibration")
+    P --> Va("Value")
+    P --> I("Indices")
+    I --> CC("Calibrated coordinate")
+    C --> CC
 
 figure: /figures/spatial_calibration.png
 figure_legend: Spatial calibration and size measurements

diff --git a/figures/resources/spatial_calibration.png b/figures/resources/spatial_calibration.png
diff --git a/figures/resources/spatial_calibration.pptx b/figures/resources/spatial_calibration.pptx
diff --git a/figures/spatial_calibration.png b/figures/spatial_calibration.png
diff --git a/image_data/xy_8bit_labels__mitocheck_incenp_t1.tif b/image_data/xy_8bit_labels__mitocheck_incenp_t1.tif
diff --git a/image_data/xy_8bit_labels__mitocheck_incenp_t70.tif b/image_data/xy_8bit_labels__mitocheck_incenp_t70.tif