## 4.1 Intensities of Red, Green and Blue

• Please upload the file ‘golgi-frame_all.tif’ into Colab before you do the following. View $$\longrightarrow$$ Table of Contents $$\longrightarrow$$ Files $$\longrightarrow$$ UPLOAD

The following Python code finds the total intensity for the three RGB colours10. We will then plot the variation of the RED and GREEN intensities with time.

img = io.imread('golgi-frame_all.tif')
no_of_frames, no_of_rows, no_of_columns, no_of_layers = img.shape       # Get video info

#--------------------------------------------------------------------------------#
#                                                                                #
#                                Extract the Data                                #
#                                                                                #
#--------------------------------------------------------------------------------#
intense_data = np.zeros([3,17])                                        # To hold the data for each frame.
#17 frames, 3 layers each
for frame in range(no_of_frames):                                       # Go through All frames
for layer in range(no_of_layers):                                   # Go through All layers for each frame
intense_data[layer,frame] = np.sum(img[frame,...,layer])

#--------------------------------------------------------------------------------#
#                                                                                #
#                               Normalize the Data                               #
#                                                                                #
#--------------------------------------------------------------------------------#
# I.e. use largest value to divide throughout to get 1 as the maximum

max_intensity = np.max(intense_data)                                   # What is the maximum
intense_data = intense_data/max_intensity                             # Normalize

#--------------------------------------------------------------------------------#
#                                                                                #
#                                 Plot the Data                                  #
#                                                                                #
#--------------------------------------------------------------------------------#
layer_names = ['Red','Green','Blue']                                    # Labels for the layers

plt.clf()
for layer in range(no_of_layers):
plt.plot(intense_data[layer],label = layer_names[layer],color=layer_names[layer])

plt.legend()
plt.grid()
plt.xlabel('Frame')
plt.ylabel('Total intensity (AU)')
plt.show()

1. E.g. the RED intensity is the sum of all the RED counts in a frame.