Surgical_instruments_pilot: A Jupyter Notebook repository from yrodriguezmd

Object Detection for Surgical Instruments

Objective:

Develop an application that can reliably locate and identify surgical instruments in an image.

Summary of Methodology:

1. Develop a teacher model

a. Create labelled data (n = 500 - 1000)

  i.   Generate pseudolabels using a pretrained model (VFnet, RetinaNet in Airctic/IceVision) (n=100)
  
  ii.  Refine annotation using annotation tool in Roboflow
  
  iii. Iteratively generate pseudolabels by passing through fine-tuned models (n= 100 per iteration)

b. At labelled data n = 500 - 1000, create pseudolabels by running unlabelled images (n= 4000) through:

  i.  VFnet with pretrained weights
  
  ii. VFnet with random initialized weights

2. Develop a student model

  i.  Merge the labelled data (from 1.a.) with the pseudolabels (from 1.b)
  
  ii. Run through a VFnet configuration with randomly initialized weights

3. Test on held-out test dataset (n= 500)

4. Deploy

Surgical_instruments Repository

A collection of images, annotations and notebooks for project development of a surgical instrument detection tool

A. PILOT

1. Manual_Labelling

a. Roboflow

i. Instruments curl, parse

Focus: Using images manually gathered from the net, annotated in roboflow, exported tensorflow OD csv format via curl; parsing done; n_original =10, n_filename = 21, n_class = 13

b. CVAT

B. PROJECT

Datasets For Pseudolabelling

1. Surg100

Contains: Downloaded images, comprising of 15 classes, at 5-7 representatives per class, N=100; for inference and pseudolabel generation, refining of annotation.

Classes (Supercategories/ Name):

Scalpel:

Scalpel

Scissors:

Mayo_metz

Iris

Potts

Forceps:

Forceps

Clamp:

Hemostat

Bulldog

Towel_clip

Needle_holder:

Castroviejo

Retractor:

Weitlaner

Richardson

Army_navy

Suction:

Frazier

Yankauer

Needle:

Needle

Refined annotations downloaded in COCO JSON form and RetinaNet CSV form.

Surg200

Mixed surgical instruments, N=100, n_classes = 15, n_supercategories = 8.

--> Merge Surg100 and Surg200, fine tune Vfnet

Annotation Tool insights

initial label assist not good, but as progress through the process, suggestions become better
train/ val/ test split representatives are preserved when projects are merged

yrodriguezmd/Surgical_instruments_pilot