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Science and technology

Getting began with a TensorFlow surgical procedure classifier with TensorBoard knowledge viz

The most difficult a part of deep studying is labeling, as you may see partly one in all this two-part sequence, Learn how to classify images with TensorFlow. Proper coaching is crucial to efficient future classification, and for coaching to work, we’d like a lot of precisely labeled knowledge. In half one, I disregarded this problem by downloading three,000 prelabeled photographs. I then confirmed you learn how to use this labeled knowledge to coach your classifier with TensorFlow. In this half we’ll prepare with a brand new knowledge set, and I will introduce the TensorBoard suite of information visualization instruments to make it simpler to know, debug, and optimize our TensorFlow code.

Given my work as VP of engineering and compliance at healthcare expertise firm C-SATS, I used to be keen to construct a classifier for one thing associated to surgical procedure. Suturing appeared like an awesome place to begin. It is instantly helpful, and I understand how to acknowledge it. It is helpful as a result of, for instance, if a machine can see when suturing is happening, it could actually robotically establish the step (section) of a surgical process the place suturing takes place, e.g. anastomosis. And I can acknowledge it as a result of the needle and thread of a surgical suture are distinct, even to my layperson’s eyes.

My purpose was to coach a machine to establish suturing in medical movies. 

I’ve entry to billions of frames of non-identifiable surgical video, lots of which include suturing. But I am again to the labeling downside. Luckily, C-SATS has a military of skilled annotators who’re specialists at doing precisely this. My supply knowledge have been video recordsdata and annotations in JSON.

The annotations seem like this:

        "annotations": [
                "endSeconds": 2115.215,
                "label": "suturing",
                "startSeconds": 2319.541
                "endSeconds": 2976.301,
                "label": "suturing",
                "startSeconds": 2528.884
        "durationSeconds": 2975,
        "videoId": 5
        "annotations": [
        // ...and many others...

I wrote a Python script to make use of the JSON annotations to resolve which frames to seize from the .mp4 video recordsdata. ffmpeg does the precise grabbing. I made a decision to seize at most one body per second, then I divided the overall variety of video seconds by 4 to get 10okay seconds (10okay frames). After I discovered which seconds to seize, I ran a fast check to see if a selected second was inside or exterior a section annotated as suturing (isWithinSuturingSection() within the code under). Here’s

# Grab frames from movies with ffmpeg. Use a number of cores.
# Minimum decision is 1 second--this is a shortcut to get much less frames.
# (C)2017 Adam Monsen. License: AGPL v3 or later.
import json
import subprocess
from multiprocessing import Pool
import os
frameList = []
def isWithinSuturingSection(annotations, timepointSeconds):
    for annotation in annotations:
        startSeconds = annotation['startSeconds']
        endSeconds = annotation['endSeconds']
        if timepointSeconds > startSeconds and timepointSeconds < endSeconds:
            return True
    return False
with open('available-suturing-segments.json') as f:
    j = json.load(f)
    for video in j:
        videoId = video['videoId']
        videoDuration = video['durationSeconds']
        # generate many ffmpeg frame-grabbing instructions
        begin = 1
        cease = videoDuration
        step = Four # Reduce to seize extra frames
        for timepointSeconds in xrange(begin, cease, step):
            inputFilename = '/residence/adam/Downloads/suturing-videos/.mp4'.format(videoId)
            outputFilename = '-.jpg'.format(video['videoId'], timepointSeconds)
            if isWithinSuturingSection(video['annotations'], timepointSeconds):
                outputFilename = 'suturing/'.format(outputFilename)
                outputFilename = 'not-suturing/'.format(outputFilename)
            outputFilename = '/residence/adam/native/'.format(outputFilename)
            commandString = 'ffmpeg -loglevel quiet -ss -i -frames:v 1 '.format(
                timepointSeconds, inputFilename, outputFilename)
                'outputFilename': outputFilename,
                'commandString': commandString,
def grabFrame(f):
    if os.path.isfile(f['outputFilename']):
        print 'already accomplished '.format(f['outputFilename'])
        print 'processing '.format(f['outputFilename'])
        subprocess.check_call(f['commandString'].break up())
p = Pool(Four) # for my Four-core laptop computer, frameList)

Now we’re able to retrain the mannequin once more, precisely as before.

To use this script to snip out 10okay frames took me about 10 minutes, then an hour or so to retrain Inception to acknowledge suturing at 90% accuracy. I did spot checks with new knowledge that wasn’t from the coaching set, and each body I attempted was accurately recognized (imply confidence rating: 88%, median confidence rating: 91%).

Here are my spot checks. (WARNING: Contains hyperlinks to pictures of blood and guts.)

How to make use of TensorBoard

Visualizing what’s taking place underneath the hood and speaking this with others is at the very least as exhausting with deep studying as it’s in another form of software program. TensorBoard to the rescue! from part one robotically generates the recordsdata TensorBoard makes use of to generate graphs representing what occurred throughout retraining.

To arrange TensorBoard, run the next contained in the container after operating

pip set up tensorboard
tensorboard --logdir /tmp/retrain_logs

Watch the output and open the printed URL in a browser.

Starting TensorBoard 41 on port 6006
(You can navigate to

You’ll see one thing like this:

I hope this can assist; if not, you may at the very least have one thing cool to indicate. During retraining, I discovered it useful to see underneath the “SCALARS” tab how accuracy will increase whereas cross-entropy decreases as we carry out extra coaching steps. This is what we wish.

Learn extra

If you’d wish to study extra, discover these sources:

Here are different sources that I utilized in scripting this sequence, which can show you how to, too:

If you want to speak about this subject, please drop by the ##tfadam topical channel on Freenode IRC. You may email me or go away a remark under.

This sequence would by no means have occurred with out nice suggestions from Eva Monsen, Brian C. Lane, Rob Smith, Alex Simes, VM Brasseur, Bri Hatch, and the editors at

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