(semi-) automatic recognition of microorganisms in water k. rodenacker, p. gais 2, u. jütting and...
TRANSCRIPT
![Page 1: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/1.jpg)
(S(Semiemi-) A-) Automaticutomatic RRecognitionecognition ofof MMicroorganismsicroorganisms inin W Waterater
K. Rodenacker, P. Gais2, U. Jütting and B. A. HenseGSF-IBB, 2GSF-Patho, Neuherberg, Germany
![Page 2: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/2.jpg)
Karsten Rodenacker GSF-IBB AG2 2
ContentContent Introduction Material Methods Results Summary and Discussion
![Page 3: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/3.jpg)
Karsten Rodenacker GSF-IBB AG2 3
IntroductionIntroduction Studies on the
effects of toxicants on the biocenosis of aquatic model ecosystem Characterization of
plankton commun.(identification, counting of phyto-plankton)
![Page 4: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/4.jpg)
Karsten Rodenacker GSF-IBB AG2 4
MaterialMaterial Preparation
Container of semi-permeable LDPE tubes containing the test substance
Water column
![Page 5: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/5.jpg)
Karsten Rodenacker GSF-IBB AG2 5
MaterialMaterial Data gathering
Sedimentation Slide preparation Microscopy
![Page 6: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/6.jpg)
Karsten Rodenacker GSF-IBB AG2 6
MaterialMaterial Data processing
with QWin, QUIPS Scan path and
autofocus Digitization and
storage~45 sec/image
![Page 7: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/7.jpg)
Karsten Rodenacker GSF-IBB AG2 7
MaterialMaterial Some organisms to
be classified
GYLA PEUM MIPU CRER
HUKU OOMA CHAC CRMA
QULA KICO ZIGA ACMX
CLSA PLGE ZIGA
![Page 8: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/8.jpg)
Karsten Rodenacker GSF-IBB AG2 8
MethodsMethods Data processing
with IDL Image segmentation Feature extraction Classification Re-classification
and training
![Page 9: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/9.jpg)
Karsten Rodenacker GSF-IBB AG2 9
MethodsMethods Image
segmentation:(two-step method) Rough
segmentationimage threshold
Fine segmentationobject threshold(RATS)
Unbiased count(forbidden line)
![Page 10: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/10.jpg)
Karsten Rodenacker GSF-IBB AG2 10
MethodsMethods Feature extraction
Shape geometrical analytical (Fourier,
curvature) topological (convex
hull, distance map) algebraic (moments,
PCA)
![Page 11: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/11.jpg)
Karsten Rodenacker GSF-IBB AG2 11
MethodsMethods Feature extraction
Extinction(optical density)
histogram featuresmean (M1), SD (M2), skewness (M3) etc.
moments (algebraic)
transmitted light optical density
Histogram of values of transmitted light
![Page 12: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/12.jpg)
Karsten Rodenacker GSF-IBB AG2 12
MethodsMethods Classification
Hierarchical tree classifier based on stepwise linear discriminance analysis
ALL
GYLA
KICO
OOMA
CLSA
CHAC
CRER
PEUM
Artefacts
![Page 13: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/13.jpg)
Karsten Rodenacker GSF-IBB AG2 13
MethodsMethods Re-Classification
Interaction Control Correction Training
![Page 14: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/14.jpg)
Karsten Rodenacker GSF-IBB AG2 15
Preliminary ResultsPreliminary Results Comparison of
manual and automatic procedure
![Page 15: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/15.jpg)
Karsten Rodenacker GSF-IBB AG2 16
Summary and Summary and DiscussionDiscussion
Difficulties or failures Separate softwares
(Qwin, IDL) Autofocus
automized microscope
Segmentation Unlimited number of
organism groups
![Page 16: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/16.jpg)
Karsten Rodenacker GSF-IBB AG2 17
Summary and Summary and DiscussionDiscussion
Successes Effective training
system for biologists AND computer scientists
Very good collaboration between the different faculties
![Page 17: (Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany](https://reader035.vdocuments.us/reader035/viewer/2022062423/56649c7b5503460f9492eb20/html5/thumbnails/17.jpg)
Karsten Rodenacker GSF-IBB AG2 18
Summary and Summary and DiscussionDiscussion
Outlook Fluorescence Multiple focal depth Type specific object
shape features (dominant feature points)
Texture object features