LabelSlide is a slide annotation tool and label object bounding boxes in virtual slides (generally used in pathology)

LabelSlide is based on B/S structure and written in Python.
Using OpenSlide to read the virtual slides and create DeepZoom Image.
Then view the zoomable image in browser by OpenSeadragon.
Adding Fabric.js canvas to draw label box overlaying the OpenSeadragon viewer.
The webpage build with Bootstrap

Python

pip install -r requirements.txt
python label_slide.py

access 127.0.0.1:5000 (as default)

If show error "Could not find module 'libopenslide-0.dll'". Please download libvips and unzip to bin folder

There's two config file.

app_config.py
Including HOST, PORT for the app and the SLIDE_CONFIG for slide config(the file path of config.yaml).
ps: parameter name must be uppercase

config.yaml
Containing the following parameters
slide_dir: the directory where slides are kept. label_dir: the directory where the annotation will be saved to.
class: pre-defined classes including id, name and color.

For example:

slide_dir: D:\Dataset\slides
label_dir: D:\Dataset\labels
class:
- id: 0
  name: A
  color: '#2196f3'
- id: 1
  name: B
  color: '#0014a8'

ps: the class id must be integer and the color must be hex format.
All content in config.yaml could be modified from webpage

In theory, the tool can read virtual slides in several formats because using OpenSlide:

• Aperio (.svs, .tif)
• Hamamatsu (.vms, .vmu, .ndpi)
• Leica (.scn)
• MIRAX (.mrxs)
• Philips (.tiff)
• Sakura (.svslide)
• Trestle (.tif)
• Ventana (.bif, .tif)
• Generic tiled TIFF (.tif)

But only try MIRAX(.mrxs) under development.
If you want to read slide in other formats, you should modify code in label_tool.py by yourself.

Support rectangle box and polygon box currently.

Hotkeys

Annotation file
One slide corresponds to one annotation file.
Take annotation for MIRAX (.mrxs) as an example

slide: C20200174
boxes:
- class: 0
  type:rect
  x: 30749
  y: 70121
  w: 468
  h: 434
- class: 1
  type: poly
  points:
  - x: 33813
    y: 62176
  - x: 33931
    y: 62571
  - x: 34099
    y: 62308

x,y is the top left pixel and w,h is the region size in the level 0 reference frame(highest resolution)

• OpenSlide
• OpenSeadragon
• OpenSeadragon-Scalebar
• Fabric.js
• Bootstrap

LGPL-2.1 License