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Tiled Data Reconstruction and Correction

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  1. Tiled Data Reconstruction and Correction By Abhishek Singh RajheshBabu, Bangalore Revanna And Joel Solomon, Bula

  2. Contents • Introduction • ImageJ • Image Stitching • Plugin Usages • Future Work • Conclusion • Queries?

  3. Introduction • There is an increasing demand to image large biological specimen at high resolution, typically those specimen which do not fit in the field of view of the microscope. • Biologists use Confocal, Bright field or Electron microscopes equipped with motorized stages to stepwise image large areas using high magnifications. • The acquired image tiles have to be combined into one final output image by a process usually referred to as Image Stitching.

  4. About ImageJ • ImageJ is public domain, Java based Image processing program that was designed with an open architecture that provides extensibility via Java plug-ins and recordable macros. • User-written plug-ins make it possible to solve many image processing and analysis problems. •  It can read many image formats including TIFF,GIF,PNG,JPEG as well as raw formats. • ImageJ supports image stacks, a series of images that share a single window, and it is multithreaded, so time-consuming operations can be performed in parallel on multi-CPU hardware.

  5. Image Stitching • Image Stitching is the process of the combining multiple images to form a single high resolution image. • Image stitching in image j has 2 plugins • Pairwise Stitching – The input is only 2 images at a time. • Grid Stitching – The input is an arbitrary collection or grid of images.

  6. Input tiff format file

  7. Pairwise Stitching • It queries the two images that you intend to stitch. The images can contain rectangular ROIs which limit the search to those areas, however the full images can be stitched. • Once you have selected the two images to be stitched, it will show the actual Pairwise stitching dialog. • The dialog will depend completely on the dimensions of the images selected, and you have to note that the RGB input images will be converted to 8bit composite images.

  8. Procedure • Pairwise Image stitching : input two images • Linear Blending : Smooth adjustment • Average : Compute average intensity • Max Intensity • Min Intensity • Overlay into composite : Channel separation • Computation parameters : Save memory • Thresholding

  9. Dialog of Pairwise Stitching

  10. Example of Pair-wise stitching

  11. Grid/Collection Stitching • This plugin is able to stitch an arbitary collection or grid of images whether it is 2d-5d images, as long all images are of same type. • In contrast to Pairwise stitching, this plugin will load and potentially save the images from/to the harddisk. • It’s always better to give the approrimate values of the tiles of the tiles, this will reduce the computational effort of the Grid stitching plugin. • If the layout of the tiles is not known, then the Stitching will figure out on it’s own, but this takes time.

  12. The first dialog queries the type image collection or image grid that you want to assemble. • For each major type, there are many sub-types you can choose from. The various options are : • Grid : row by row • Grid : column by column • Grid : snake by rows • Grid : snake by columns • Filename defined positions • Unknown positions • Positions from File

  13. First dialog and second dialog

  14. Code Snippet Input

  15. Sample Slices for stitching

  16. Output Two images stitched

  17. Output Four images stitched

  18. 4 slices stitched in a column

  19. 4 slices stitched in a row

  20. Brightness Control Using Slider

  21. Brightness Control

  22. Libraries for plugins

  23. Main classes and plugins

  24. Conclusion and future work • We have to have to work on alignment and scaling. • “Out of memory” problem. • We have implemented the conversion of .oib image format to .tiff using bio-format reader. • How to adjust the correct brightness in the stitched images. • Also work on image blending and overlapping .

  25. References • http://drosophila.biology.kent.edu/users/rclement/resources/Jan30-2014.pdf • http://fiji.sc/Image_Stitching • http://www.cs.bath.ac.uk/brown/autostitch/autostitch.html • http://bioinformatics.oxfordjournals.org/content/25/11/1463.full.pdf

  26. Thank you!!