diff --git a/.DS_Store b/.DS_Store index 0c53ab9..eb4bb33 100644 Binary files a/.DS_Store and b/.DS_Store differ diff --git a/content/docs/.DS_Store b/content/docs/.DS_Store index 10bcdff..d4c9556 100644 Binary files a/content/docs/.DS_Store and b/content/docs/.DS_Store differ diff --git a/content/docs/processing/z_proj_tut1.md b/content/docs/processing/z_proj_tut1.md deleted file mode 100644 index f5ba5e6..0000000 --- a/content/docs/processing/z_proj_tut1.md +++ /dev/null @@ -1,102 +0,0 @@ -+++ -title = "My notebook title" -date = "2018-06-01" -author = "firstname lastname" -categories = ["category1", "category2"] -tags = ["tag1", "tag2", "tag3"] -+++ - - -# Post title - - -```python -from skimage import data -import matplotlib.pyplot as plt -import numpy as np - -image = data.cells3d() - -``` - - -```python -print (image.shape) -``` - - (60, 2, 256, 256) - - - -```python -plt.imshow(image[40,1,:,:]) - -``` - - - - - - - - - -{{< figure src="media/SD_fluor.png" alt="Image showing change of SD in z-stacks" caption="Figure 1: Different z-stacks of a GFP fluorescent cell, demonstrating how the standard deviation (SD) varies with focus. Each stack shows a detailed view of the cell's border, illustrating how pixel intensities differ more sharply when the image is in better focus." >}} - -![png](output_4_1.png) - - - - -```python -nucl_img_all = image[:,1,:,:] -nucl_img_sel = image[25:40,1,:,:] -print(nucl_img.shape) - -mean_nucl_img = np.mean(nucl_img, axis=0) -mean_nucl_sel = np.mean(nucl_img_sel, axis= 0) -``` - - (60, 256, 256) - - - -```python -plt.imshow(mean_nucl_img) -``` - - - - - - - - - - -![png](output_6_1.png) - - - - -```python -plt.imshow(mean_nucl_sel) -``` - - - - - - - - - - -![png](output_7_1.png) - - - - -```python - -``` diff --git a/static/content/z_proj_tut1/output_4_1.png b/static/content/z_proj_tut1/output_4_1.png deleted file mode 100644 index 37dbac4..0000000 Binary files a/static/content/z_proj_tut1/output_4_1.png and /dev/null differ diff --git a/static/content/z_proj_tut1/output_6_1.png b/static/content/z_proj_tut1/output_6_1.png deleted file mode 100644 index 7d750d8..0000000 Binary files a/static/content/z_proj_tut1/output_6_1.png and /dev/null differ diff --git a/static/content/z_proj_tut1/output_7_1.png b/static/content/z_proj_tut1/output_7_1.png deleted file mode 100644 index f452a6b..0000000 Binary files a/static/content/z_proj_tut1/output_7_1.png and /dev/null differ