Measuring in Time

Biomedical Image Analysis in Python

Stephen Bailey

Instructor

Ejection fraction

$$ Ejection\ Fraction = \frac{LV_{max} - LV_{min}}{LV_{max}} $$

heart-beat

Ejection fraction

Procedure

Segment left ventricle
For each 3D volume in the time series, calculate volume
Select minimum and maximum
Calculate ejection fraction

Calculate volume for each time point

# Stored in (t,z,x,y) format
vol_ts.shape
labels.shape

(20, 12, 256, 256)
(20, 12, 256, 256)

timeseries-plot

# Calculate voxel volume in mm^3
d0,d1,d2,d3=vol_ts.meta['sampling']
dvoxel = d1 * d2 * d3

# Instantiate empty list
ts = np.zeros(20)

# Loop through volume time series
for t in range(20):

    nvoxels=ndi.sum(1,
                    labels[t], 
                    index=1)

    ts[t] = nvoxels * dvoxel

plt.plot(ts)
plt.show()

Calculate ejection fraction

min_vol = ts.min()
max_vol = ts.max()

ejec_frac = (max_vol - min_vol) / max_vol

ejec_frac

0.58672

maximum-minimum-side-by-side

Let's practice!

Biomedical Image Analysis in Python