LBNL DSD Whole Frog Project

Time 2020-12-14 14:04:08

Web Name: LBNL DSD Whole Frog Project

WebSite: http://froggy.lbl.gov

ID:133892

Keywords:

DSD,LBNL,Whole,

Description:

Technique for acquiring and processing the frog dataFor a variety of technical reasons relating to differences betweenmammalian and amphibian physiology, the resolution of MRI images of afrog were not good enough to clearly separate internal structures.A high resolution data set was obtained by a mechanicalsectioning technique that gave sufficient resolution to see detaildown to the level of large nerves.Examples of mechanical slice data:For a report on the mechanical sectioning and associated data collection issues,please seeWhole Frog Technical Report.Examples of reconstructions of other organismsHigh resolution MRI studies of several plants were done as part of this project, withan orange forming the basis of the 3D reconstruction study unit.Images of reconstructed tomato:3D reconstruction of the frog's anatomyExamples of frog reconstructions:Example 2 of frog reconstruction. (TIF file)Example 3 of frog reconstruction. (TIF file)Rotating, transparent frog movieThe following are two different encodings of the same sequence.MPEG movie of frog rotating (769 KBytes)Quicktime (JPEG compressed) movie of frog rotating (1,862 KBytes)Available image data Two kinds of data are used in the 3D reconstructions: slice images (example slice),and masks (example mask).Slice images are a sequence of sections through the object of interest. Theseslices may be obtained directly as in mechanical slicing, or by tomographicreconstruction. The masks are a geometric representation of objects ofinterest and are obtained by "segmentation" of the images. (This can be donemanually, or using image processing techniques.)The following describes how to get all of the data that went into theimages and reconstructions illustrated in this document.The "data" behind the 3D models (e.g. of the frog) are images of slicesthrough the original object, and "masks" that define various regions ofinterest (anatomical systems, in the case of the frog).Monochrome slice imagesTheslice image dataare in two different formats: "raw" (no header)monochrome images with a file format: each pixel is an unsigned byte, and thescan lines are stored row-wise. For each data set there is a file called *.hdthat describes the number and size of the images. The slice image filescontain all slices for a given organism. For example, the frog slice imagedata set is 470 x 500 x 1Byte x 136 images. So each 500 bytes from thisdataset represents one scan line of the slice image.This is the original data obtained by cryotome slicing of the frog. Theslices are available both forindividual viewingTIFFformat, using the TIFF LZW compression option (approximately 900K apiece),and in bulk as azip file (~120 Mbytes).ratdata are only available as MRI - the rat dataset is not high quality.TheMRI datacorresponding to the section data for the frog is alsonot of very high quality. (Thespeculation is that iron pigments in the frog's skin interfere with the MRI.)Many of the MRI images (as the tomato is) may require normalizationor histogram equalization in order to "see" much in an image displayed on thescreen. For example:The masks are available asanimated GIF'ssuitable for viewing, and asmulti-page TIFF filessuitable for downloading. The TIFF files were created with the TIFF optionto LZW compress the mask data.Some Sun rasterfile screen dumps of 3D reconstructions done by raycastingare stored in "*.IMAGES.tar" under thelinksgiven above.CREDITSThis work was done at Lawrence Berkeley National Laboratory in 1993-1995,and was sponsored at that time by the U. S. Dept. of Energy, Energy ResearchDivision,Mathematical,Information, and Computational Sciences Division, John Cavallini programmanager.Lawrence Berkeley National Laboratory is operated by the University ofCalifornia for DOE under contract DE-AC03-76SF00098 .Thanks to the many people that made this project possible:LBL Center for Science and Engineering EducationRollie Otto, DirectorEileen EngelSummer teachers (TRAC program)Darrel RichterV. NewtonAna L. PadillaBea AlexanderMiguel RivasKris SahuDr. Tom Budinger (for showing us the potential of high resolution MRI)Mark Roos and Sam Wong (who did the MRI imaging)Katie Brennan (for "Fluffy")Anat Biegon (for the use of her Cryotome)University of California, Berkeley, Biology Dept.Dr. Paul Licht (a specialist in amphibian anatomy, for his consulting)Craig Logan (anatomy student who did most of the frog masks)Computer Science StudentsWing Nip, San Francisco State University (now at Sun Microsystems)

TAGS:DSD LBNL Whole 

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