A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project A Semi-Automatic System for...
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Transcript of A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project A Semi-Automatic System for...
A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
A Semi-Automatic System for Pollen Recognition
1- INRIA, Sophia-Antipolis, France2- LASMEA, Blaise Pascal University, Clermont-Ferrand, France3- University of Córdoba (UCO), Spain4- Autonomous University of Barcelona (UAB), Cerdanyola del Vallès,Spain
Alain Boucher1, Régis Tomczak2, Pablo Hidalgo3, Monique Thonnat1, Jordina Belmonte4,
Carmen Galan3 and Pierre Bonton2
2A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Introduction
• Goal: Help the technician identify and count per types the pollen grains
• Pollen concentration can be used– for public report
– for the forecast system
3A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
System Architecture
4A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
System Hardware
A light microscope is driven automatically by a computer
5A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Material and Methods
• System Hardware:– Light microscope Light microscope – 3 axes micro-positionning device3 axes micro-positionning device– CCD colour cameraCCD colour camera– Image acquisition cardImage acquisition card– PC computerPC computer
• Pollen slides are prepared by technicians– Pollen grains are sampled using Hirst traps– Pollen grains are coloured with fuchsine
• Pollen grains are observed with a magnification of 60x
6A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Man-Machine Interface
The system can work in supervised or automatic mode
7A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Pollen Grain Detection and Localisation
Segmentation Localisation
Automatic pollen grain detection
8A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Pollen Grain Extraction
• 3D acquisition of pollen grains– set of images at different depths
Features may appear on different heights
• 100 optical sections• step = 0.5 microns
For each grain
9A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Main Pollen Types Studied and Similars
PoaceaeOlea ParietariaCupressaceae
Populus BrassicaceaeFraxinusLigustrumPhillyreaSalix
BroussonetiaMorusUrtica membranacea
CeltisCoriaria
10A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Pollen Grain Recognition
• Goal is to identify the typeidentify the type of the pollen grain from 3D images3D images
• Grain recognition is done following two stepstwo steps:
– Compute global measures
– Search for specific characteristics
• Pollen knowledgePollen knowledge is used to identify each grain
– Palynology (apertures, reticulum, size, …)
– Aerobiology (flowering period)
11A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Palynological Knowledge
• The system tries to mimic the palynologists
• Pollen knowledge is used to identify each grain
• Knowledge sources from
– Palynology
– Aerobiology
12A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Compute Global Measures
• Help to decide which grain characteristics to look for
• Measures:– Diameter
– Colour (RGB)
– Shape
– ...
Diameter (microns) vs Mean blue colour
13A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Example: Broken Cupressaceae Grains
– Broken Cupressaceae grains are detected by shape:• Form factor: 4 surface / perimeter ²
• Convexity ratio: grain surface / convex hull surface
Broken grain Convex hull
14A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
– Only search for possible characteristics
– Found characteristics help to look for others
Search Pollen Characteristics
Image Full Grain
Inside Exine
Blur analysis vs Image number
15A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Example: Poaceae Pore
Image 35 /100 Image 50 / 100 Image 65 / 100 Image 80 / 100
16A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Example: Cupressaceae Cytoplasm
Image 40 / 100 Image 50 / 100 Image 60 / 100
17A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Example: Olea Reticulum Detection
– The reticulum is located at top (or bottom) surface of the grain
– Steps to follow:• Check if the pollen is reticulated
• Localize the reticulum
• Analyze the reticulum
18A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Example: Olea Reticulum Analysis
– Find the image with the sharpest reticulum
– Extraction of a zone with reticulum (muri & lumina)
– Extraction of some lumina (clear or dark)
– Analysis of size and shape of the lumina
19A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Pollen Counting
• Final output: pollen concentration in the air– pollen count per type
– hourly, dayly or weekly concentration
• Unknown grains are reported to the technicians
• Output can be used– for public report
– for the forecast system
20A Semi-Automatic System for Pollen RecognitionA.S.T.H.M.A. Project
Conclusion
• Hard to give classification results so far– With only the 4 chosen pollen types, recognition of almost 100%, but
need more tests including other similar pollen types
• Database of more than 350 digitized pollen grains350 digitized pollen grains (30 different pollen types)
• Steps of development :– 4 allergenic pollen types (Cupressaceae, Olea, Parietaria, Poaceae)
– 11 similar pollen types (Populus, Fraxinus, Morus, Celtis, …)
– 15 other frequent pollen types (Betula, Quercus, Pinus, …)