Image Processing with KNIME
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- Rosalind Kennedy
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1 Image Processing with KNIME
2 Who we are?! Martin Horn (+49) Z815 Active Segmentation Christian Dietz (+49) Z815 Active Classification
3 1. Big Picture Scientific Image Processing 2. KNIME Image Processing (KNIP) The Plugin KNIME Developer Training 3
4 The Zoo of Image Processing Tools Development ImgLib OpenCV MatLab NumPy VTK VIGRA Processing UI ImageJ KNIP Fiji CellProfiler Ilastik CellCognition Icy Photoshop Handling OMERO BioFormats = Single, individual, case specific, incompatible solutions KNIME Developer Training 4
5 The Zoo of Image Processing Tools Which combination should I use? Reusability? Interoperability? Many wheels out there KNIME Developer Training 5
6 The Zoo of Image Processing Tools Development ImgLib OpenCV MatLab NumPy VTK VIGRA Processing UI ImageJ2/Fiji2 KNIP CellProfiler Icy Ilastik CellCognition Photoshop Handling OMERO BioFormats = Standardized Java Framework for Scientific Image Processing KNIME Developer Training 6
7 SciJava Overview KNIP (Konstanz) ImgLib (MPI Dresden) Fiji/ImageJ (Madison) BioFormats (Madison) OMERO (Dundee) KNIME Developer Training 7
8 ImgLib2 SciJava Developed at MPI-CBG Dresden Generic Framework for data (image) processing algorithms and data-structures KNIME Developer Training 8
9 ImageJ SciJava ImageJ Wayne Rasband (National Institutes of Health) Popular, highly interactive image processing program Many plugins available KNIME Developer Training 9
10 FIJI SciJava ImageJ/FIJI Extension of ImageJ1 with plugin-update mechanism ImageJ2 New Version of ImageJ based on ImgLib2 IJ1 plugins still work KNIME Developer Training 10
11 SciJava - OME Open Microscopy Environment Joint project Dundee, Baltimore, Harvard Medical School and LOCI Open tools to support data management for biological light microscopy Standardized file-format (OME-XML) KNIME Developer Training 11
12 OMERO SciJava - OME Tools for storing (database), visualizing, managing and annotating images and metadata BioFormats Library for reading and writing > 120 microscopy file formats KNIME Developer Training 12
13 Basic information SciJava - KNIP KNIME Image Processing Basic data structures: ImgLib2 High-throughput screening Fast prototyping Understandable workflows KNIME Developer Training 13
14 Who? KNIME Image Processing (KNIP) Martin Horn (University of Konstanz) Christian Dietz (University of Konstanz) Thorsten Rieß (University of Konstanz) Slawek Mazur (BioQuant Heidelberg) KNIME User Meeting 14
15 KNIME Image Processing (KNIP) Who? Students Felix Schoenenberger (University of Konstanz) Clemens Muething (University of Konstanz) Jan-Dirk Verbeek (University of Konstanz) Jens Metzner (University of Konstanz) Maximilian Ortwein (University of Konstanz) several others KNIME User Meeting 15
16 Why Image Processing with KNIP? Analysis of huge image data sets (HCS) Further analysis of the data Machine learning Visualization Statistics everything which comes with KNIME KNIME User Meeting 16
17 Image IO in KNIP? Image Reader using Bio-Formats 122 supported formats OMERO Image Reader (experimental) Images from the OMERO image data base Image Writer using Bio-Formats 11 supported formats (e.g. tif, jpeg, png, ometiff, ) KNIME User Meeting 17
18 KNIP - How images are handled? KNIME User Meeting 18
19 KNIME User Meeting 19
20 KNIP - How images are handled? KNIME User Meeting 20
21 KNIP - How images are handled? KNIME User Meeting 21
22 What s an image in KNIP? KNIME User Meeting 22
23 What s an image in KNIP? KNIME User Meeting 23
24 What s an image in KNIP? KNIME User Meeting 24
25 What s an image in KNIP? time KNIME User Meeting 25
26 KNIP - How to inspect images? KNIME User Meeting 26
27 KNIP How to inspect images? KNIME User Meeting 27
28 KNIP How to inspect images? KNIME User Meeting 28
29 KNIP - How to process images? KNIME User Meeting 29
30 KNIP - How to process images? KNIME User Meeting 30
31 KNIP - How to process images? KNIME User Meeting 31
32 KNIP - How to process images? KNIME User Meeting 32
33 KNIP - How to process images? KNIME User Meeting 33
34 KNIP - How to process images? KNIME User Meeting 34
35 KNIP - How to segment images? KNIME User Meeting 35
36 KNIME User Meeting 36
37 How to represent region of interests? KNIME User Meeting 37
38 KNIP - Feature calculation KNIME User Meeting 38
39 KNIME User Meeting 39
40 KNIP - Feature calculation First order statistics Mean, Standard Deviation, Skewness, Texture features Haralick, Tamura, Geometric features Circularity, Convexity, Centroid, Size, KNIME User Meeting 40
41 KNIP - Feature calculation Shape Features Fourier Descriptors, Radial Distances, Many under development Bag of gradients, Histogram of Gradients, Zernike, KNIME User Meeting 41
42 KNIP Feature calculation KNIME User Meeting 42
43 KNIP Feature calculation KNIME User Meeting 43
44 KNIP - Feature calculation KNIME User Meeting 44
45 KNIME User Meeting 45
46 KNIP Segment Overlay KNIME User Meeting 46
47 KNIP KNIME User Meeting 47
48 KNIP So what? Some projects solved with KNIP Mitotic Index Chromosome Counting Cell-Lifecycle Classification Membrane Breakdown (ETH - Zürich) Single Molecule Tracking DNA-Repair Measurement. many more KNIME User Meeting 48
49 KNIP Chromosome Counting KNIME User Meeting 49
50 Chromosome Counting KNIME User Meeting 50
51 Chromosome Counting KNIME User Meeting 51
52 Chromosome Counting KNIME User Meeting 52
53 Chromosome Counting KNIME User Meeting 53
54 Chromosome Counting KNIME User Meeting 54
55 Chromosome Counting KNIME User Meeting 55
56 Chromosome Counting KNIME User Meeting 56
57 Chromosome Counting KNIME User Meeting 57
58 Chromosome Counting KNIME User Meeting 58
59 Chromosome Counting KNIME User Meeting 59
60 Chromosome Counting KNIME User Meeting 60
61 Chromosome Counting KNIME User Meeting 61
62 Chromosome Counting KNIME User Meeting 62
63 KNIME User Meeting 63
64 KNIP Example High-Content Screening positive negative KNIME User Meeting 64
65 High-Content Screening KNIME User Meeting 65
66 High-Content Screening KNIME User Meeting 66
67 High-Content Screening KNIME User Meeting 67
68 High-Content Screening KNIME User Meeting 68
69 High-Content Screening KNIME User Meeting 69
70 KNIME User Meeting 70
71 Some more examples KNIME User Meeting 71
72 Mitosis Classification KNIME User Meeting 72
73 Mitosis Classification KNIME User Meeting 73
74 Mitotic Index KNIME User Meeting 74
75 Mitotic Index KNIME User Meeting 75
76 Mitotic Index KNIME User Meeting 76
77 KNIP Nice to know Currently ~52 official nodes IO nodes: ~ 4 Image processing nodes ~ 25 Filter nodes ~ 6 Segmentation-related nodes ~ 10 Feature calculation nodes ~ 3 Viewer nodes ~ 4 KNIME User Meeting 77
78 KNIP Nice to know Sub-projects about to be released VTK based 3D-Viewer Sub-projects under development Tracking framework IJ2 integration Pixel-Classification OMERO integration KNIME User Meeting 78
79 KNIP What s next? Further OMERO integration Visit from OME-Team members early March Data handling Efficient data management KNIME User Meeting 79
80 ImageJ2 integration KNIP What s next? High priority! Waiting for some changes in IJ2 Tracking framework Builds up-on the network analysis framework Work in progress, some first results KNIME User Meeting 80
81 KNIP What s next? ImgLib2 synchronization Synchronizing code for de/serialization Integrating KNIPLib algorithms to ImgLib2 Refactoring KNIPLib algorithms KNIME User Meeting 81
82 KNIP Community Contributions Update site News, mailing list, SVN-Access Use the FORUM! KNIME User Meeting 82
83 KNIP How to take part? We need feedback! We are open for any suggestions, help, feature requests, bug reports KNIME User Meeting 83
84 Thank you KNIME User Meeting 84
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