Bio-Image Acquisition and Processing Facilities, from Molecules to Brain

1. Bio-Image Acquisition and Processing Facilities, from Molecules to Brain

4. • Image acquisition • Image Processing • Computer Graphics Light Magnetic Microscope resonance (µM - MM) (MM - CM) Bugnon 7-9 Fixed Dynamic Atomic Force Electron Confocal Microscope Microscope microscope ( nanoM ) ( nanoM ) (µM)

6. Program Les formats de stockage des images numériques: R. Kraftsik Fluorescence imaging in living cells: J. Staple Dynamicmeasurements of intracellular sodium in living astrocytes : Jean-Yves Chatton Time lapse video of mobile cells (Dictyostelium): C. Reymond Microscopie holographique à contraste de phase quantitative dans les cellules vivantes: P. Marquet Visualization of molecules using the atomic force microscope: S. Kasas Visualisation des images confocales en 3D avec le logiciel Imaris: N. Garin Quantification des structures 3D à partir de coupes histologiques sériées: R. Kraftsik. Analyse morphométrique des arbres neuronales et simulation: L. Tettoni Biomedical imaging: S. Clarke Autoradiographie avec NIH Image: G. Bronchti Analysis of gels and blots using Bioprint and 1D program: B. Riederer

8. Les formats de stockage des images numériques R. Kraftsik

12. Formats de fichier pour les images numériques • BMP • Photoshop EPS • EPS TIFF or EPS PICT Preview • CompuServe GIF • IFF • JPEG • MacPaint • PCX • PDF • PICT File • PICT Resource (Macintosh only) • PIXAR • PixelPaint • PNG • Raw • Scitex CT • Targa • TIFF http://www.matisse.net/files/formats.html http://www.matisse.net/files/glossary.html

13. BMP BMP is the standard Windows bitmap image format on DOS and Windows-compatible computers. When saving an image in this format, you can specify either Microsoft Windows or OS/2 format and a 1-bit to 24-bit depth for the image. For 4-bit and 8-bit images, you can also choose to use Run-Length-Encoding (RLE) compression; this compression scheme is lossless, that is, it does not discard detail from the image.

14. Photoshop EPS The Encapsulated PostScript (EPS) language file format is supported by most illustration and page-layout programs, and in most cases is the preferred format for these applications. Note that Photoshop EPS also supports transparent whites in Bitmap mode. For more information on EPS options, see Saving files in Photoshop EPS format.

15. EPS TIFF or EPS PICT Preview You can use these formats to open files saved in applications that create previews but are not supported by Adobe Photoshop (such as QuarkXPress). An opened preview file can be edited and used like any other low-resolution file.

16. CompuServe GIF The CompuServe Graphics Interchange Format (GIF) is the file format commonly used to display indexed-color graphics and images in hypertext markup language (HTML) documents over the World Wide Web and other online services. GIF is a compressed format that is designed to minimize file transfer time over phone lines. Adobe Photoshop 4.0 can save Bitmap mode, grayscale, or indexed-color images in the CompuServe GIF format. When saving an image as GIF, you can specify how the image appears as it is downloaded. Select Interlaced to display the image gradually in increasing detail as it is downloaded. The GIF89a Export command lets you specify the appearance of transparent areas in the image and save an RGB image in the GIF format. For more information, see Exporting images.

17. JPEG The Joint Photographic Experts Group (JPEG) format is commonly used to display photographs and other continuous-tone images in hypertext markup language (HTML) documents over the World Wide Web and other online services. Unlike the GIF format, JPEG retains all the color information in an RGB image. JPEG also uses a compression scheme that effectively reduces file size by identifying and discarding extra data not essential to the display of the image. Opening a JPEG image automatically decompresses it. Because it discards data, the JPEG compression scheme is referred to as lossy. This means that once an image has been compressed and then decompressed, it will not be identical to the original image. A higher level of compression results in lower image quality, while a lower level of compression results in better image quality. In most cases, compressing an image using the Maximum quality option produces a result that is indistinguishable from the original. For information on choosing JPEG options, see Saving files in JPEG format.

18. PDF The PDF format is used by Adobe Acrobat, Adobe’s electronic publishing software for Macintosh, Windows, UNIX, and DOS. You can view PDF files using the Acrobat Reader software included on your Adobe Photoshop CD-ROM. Based on the PostScript Level 2 language, PDF can represent both vector and bitmap graphics. For the purposes of representing pages, PDF pages are identical to PostScript pages, but PDF files can also contain electronic document search and navigation features. PDF files, for example, can contain hypertext links and an electronic table of contents For more information on PDF and Adobe Acrobat see the Electronic Publishing Guide included on the Adobe Photoshop Tutorial CD-ROM.

19. PICT File The PICT format is widely used among Macintosh graphics and page-layout applications as an intermediary file format for transferring files between applications. The PICT format is especially effective at compressing images that contain large areas of solid color. This compression can be dramatic for alpha channels, which often consist of large areas of white and black. When saving an RGB image in PICT format, you can choose either a 16-bit or 32-bit pixel resolution. For a grayscale image, you can choose from 2, 4, or 8 bits per pixel. If you’re using a Macintosh with QuickTime installed, you can also choose from four JPEG compression options for the file.

20. PNG The PNG format was developed as an alternative to the GIF format and, like GIF, is used for displaying images on the World Wide Web and other online services. PNG preserves all color information and alpha channels in an image and uses a lossless compression scheme to reduce file size. When saving an image in PNG format, you can choose to display the image in gradually increasing detail as it is downloaded. To do this, select Adam7 for Interlace. You can also select a filtering algorithm, which is used to prepare the image data for compression.

21. TIFF The Tagged-Image File Format (TIFF) is used to exchange files between applications and computer platforms. The TIFF format supports LZW compression, a lossless compression method that does not discard detail from the image. When you save an Adobe Photoshop image in TIFF format, you can choose to save in a format that can be read either by Macintosh or by IBM PC-compatible computers. You can also choose to compress the file to a smaller size automatically by clicking the LZW Compression check box. Adobe Photoshop reads and saves captions in TIFF files. This feature is of particular use with the Associated Press Picture Desk system, which uses the same TIFF caption fields. For information on using captions, see Adding file information.

23. TIFF 2077 KB 982X720=707040= 707Kpixel

24. JPEG 135 KB 707Kpixel