How to average summaries over multiple batches?

Do the averaging of your measure in Python and create a new Summary object for each mean. Here is what I do:

accuracies = []

# Calculate your measure over as many batches as you need
for batch in validation_set:
  accuracies.append(sess.run([training_op]))

# Take the mean of you measure
accuracy = np.mean(accuracies)

# Create a new Summary object with your measure
summary = tf.Summary()
summary.value.add(tag="%sAccuracy" % prefix, simple_value=accuracy)

# Add it to the Tensorboard summary writer
# Make sure to specify a step parameter to get nice graphs over time
summary_writer.add_summary(summary, global_step)