Download
depth intensity correction of biofilm volume data from clsm n.
Skip this Video
Loading SlideShow in 5 Seconds..
Depth Intensity Correction of Biofilm Volume Data From CLSM PowerPoint Presentation
Download Presentation
Depth Intensity Correction of Biofilm Volume Data From CLSM

Depth Intensity Correction of Biofilm Volume Data From CLSM

129 Views Download Presentation
Download Presentation

Depth Intensity Correction of Biofilm Volume Data From CLSM

- - - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

  1. Depth Intensity Correction of Biofilm Volume Data From CLSM Karsten Rodenacker1, Martina Hausner2, Martin Kühn2, Stefan Wuertz2, Sumitra Purkayastha31GSF-IBB, 2TU München, Germany3ISI, India

  2. Content • Introduction • Material and Methods • Results • Summary and Discussion

  3. Y X Z Introduction Biofilm • Biofilm

  4. Introduction Biofilm Histogram of a volume block

  5. Z Y X Introduction Biofilm • Biofilm (projection in Y) Intensity Decay in depth Surface

  6. Introduction Assumptions • Grown from surface (substratum) layer • Similar attachment of fluorescent stain, especially independent on depth • Semi-3-D arrangement (umbra type),some continuity in depth • Material distributed in all depths

  7. Z Y X Introduction First observations • Tissue section (projection in Y) Intensity decay Surface

  8. Introduction Observations • Intensity decay frequency Intensity depth

  9. Introduction Observations • Intensity decayundermorph.openingandexpon.fitting after opening 1 after opening 2 after opening 3

  10. Introduction Idea • Correction by the decay function for reliable segmentationProblem: Estimation Limitations

  11. Introduction Goals • Reliable segmentation for - Volume estimationand - estimation of local relationship of objects and of objects in clusters

  12. Introduction Partial Solutions • Iterative methodsusing approximated correction after Visser et al. and Roerdink et al. • Depth table correction (Rigaut & Vassy).

  13. Material • Hybridized biofilm - FISH(Fluor. In Situ Hybridization) - EYFP (Enh. Yellow Fluorescent Protein) • Image (volume) acquisition with Zeiss LSM410 (voxelsize .0625 µm3=.25x.25x1.(µm)3)

  14. 01 07 13 19 MaterialFlowchannel • Position ofprobe Z X Y ... Direction of flow

  15. Methods • ModelDecay caused by - the surrounding medium - occlusion (shadowing)

  16. Methods Model

  17. Methods Model

  18. Frequency Intensity Depth Methods • Depth - histograms - quantiles (p=.999) - offset by saturation - intensity decay fit

  19. Results Measurements • Volume: RED • Volume: GREEN • Volume: GREEN in RED • Volume: GREEN in dilated(RED) • Volumes in Clusters gen. from RED

  20. Results Measurements Volumes in voxel

  21. Results Measurements Gain by correction

  22. Summary and Discussion • Disadvantages • Advantages

  23. Discussion Disadvantages • Scaling problems • Verification of correction • Possible errors by deviations from the assumptions

  24. Discussion Disadvantages • Grown from surface (substratum) layer • Similar attachment of fluorescent stain, especially independent on depth • Semi-3-D arrangement (umbra type),some continuity in depth • Material distributed in all depths

  25. Discussion Advantages • Simplicity multiplicative correction (table operation) • Little computational effort a histogram above all data 255 quantiles