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Tiled data Image reconstruction and correction

Tiled data Image reconstruction and correction. Team members: Krishna Makkena Lowkya pothineni Bharath kayati. Problem: Tiled data Image reconstruction and correction. Goal: To create plugin for ImageJ for tiled image stitching and image correction. Input : OIB image sequences

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Tiled data Image reconstruction and correction

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  1. Tiled data Image reconstruction and correction Team members: Krishna Makkena Lowkyapothineni Bharathkayati

  2. Problem: Tiled data Image reconstruction and correction. • Goal: To create plugin forImageJ for tiled image stitching and image correction. • Input : OIB image sequences • Output: Stitched and brightness corrected images

  3. Steps for implementation • Step 1: Convert I/P OIB files to multi image tiff files •  Used Bio-Formats to achieve this • Step2: Split each tiff Z slice to individual images. •  Since given I/P OIB contains 135 slices, we will get 135 files for each tiff file. • Step 3: Run stitching algorithm to perform stitching.

  4. Input Files: • a)

  5. b)

  6. c) Select the input folder • d) Select the destination folder • Program will analyze and check for possible stitching . If not possible this throws a pop up saying “stitching not possible due to non similar dimensions”.

  7. e) total 9 Output tiff files will be generated as shown

  8. Step 4: Each tiff is converted to individual Z slices in corresponding folders like z1/z2 …

  9. Step 5: Now stitching of these individual slices will be done for each z index to produce 135 planes of stitched image • Example: Consider Z index as 92 ( Since this is raster scan grid stitching, refer below image for easy understanding.) • Horizontal Stitching will be done for Z1 & Z2 to get Z12 • Next Horizontal stitching will be done for Z12 & Z3 to get Z123 • Above two steps are repeated for Z4,Z5, Z6 to get Z456 & for Z7, Z8, Z9 to get Z789 • Now vertical stitching is done for Z123 & Z456 to get Z123456 • Vertical Stitching is done for Z123456 & Z789 to get Final Stitched Image for plane 92.

  10. Individual all Z92 images before stitching:

  11. After Horizontal stitching is done:

  12. Final Stitched Image for Z plane 92:

  13. References • 1 http://loci.wisc.edu/software/bio-formats • 2 http://loci.wisc.edu/software/data-browser • 3 http://www.openmicroscopy.org/site/support/bio-formats5/users/imagej/

  14. Thank You!

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