oct-lasagne

Tool for the surface annotation of retinal Optical Coherence Tomography (OCT) volumes.

Installation

git clone https://github.com/maet3608/oct-lasagne.git
cd oct-lasagne
python setup.py install

If the Kivy installation fails, install it manually:

python -m pip install docutils pygments pypiwin32 kivy.deps.sdl2 kivy.deps.glew
python -m pip install kivy

For more details see the installation instructions. If this fails as well, try to install the wheel instead. Download a matching wheel from here, e.g. Kivy-2.0.0.dev0-cp37-cp37m-win32.whl for Windows and Python 3.7, and install with

python -m pip install Kivy-1.10.1-cp36-cp36m-win_amd64.whl

Usage

USAGE:
python octlasagne.py <configfile> 

EXAMPLE 1:
cd oct-lasange/octlasange
python octlasagne.py  config.json

Configuration file

The configuration file is a file in JSON format that specifies application parameters such as

• the data directory (datadir) that contains the OCT volumes to annotate
• a scaling factor (ratio) for the width of the displayed scans
• a list of scans that are locked for annotation.

Here an example of a configuration file:

{
  "datadir": "data/oct_volumes",
  "ratio" : 4.0,
  "locked" : [0, 5, 10]
}

User interface

A short description of the user interface.

Menu

• Annotation
  • Filter: Filter for data using Pandas format, e.g. oct_id.str.startswith('oct_d15_1')
  • Add layer...: Add a new layer with the given name
  • Del layer...: Deletes the layer with the given name
  • Save : Save current annotation to annotation.pkl
  • Load backup : Loads the backup of the annotation file.
  • Show all ON|OFF : Toggle display of ALL layers
  • Show layer ON|OFF : Toggle display of current layer polyline
  • Autosave ON|OFF : Automatically save annotation when exiting

Navigation

• Button OCT >> or Cursor up: next cube
• Button << OCT or Cursor down: previous cube
• Button Scan >> or Cursor left: next B-scan within current cube
• Button << Scan or Cursor right: previous B-scan within current cube

Viewing

• Hold any mouse button and move to pan
• Use mouse wheel for zooimng in and out
• Toggle display of current annotation layer by pressing v
• Toggle display of all annotated layers by pressing a

Editing

• Add point: ALT + left mouse click
• Move point: CTRL + left mouse click
• Delete point: SHIFT + left mouse click

Timer

• start/stop timer by pressing s
• reset timer by pressing r

Exiting

Exit a dialog or the application by pressing the ESC button. The layer annotation will automatically be saved (provided Auto ON is set)

Data

The data folder must contain OCT volumes as 3D numpy arrays (dtype='uint8'), where the first axis is the B-scan, followed by rows(depth) and cols(width) of the B-scan, with image origin in the upper left corner.

Annotation

Surface annotation is stored as a pickle file in annotation.pkl, within the data folder.

In addition a backup file of the annotation in CSV format is also stored and can be loaded via the menu item Load backup