• txt         Data files such as spreadsheets in ASCII tab-delimited format.  Text files are opened in a text window with this File/open menu.  The same text files are used in other ways by the appropriate tool, for example, spreadsheets are opened as data by the Spreadsheet Tool.
• rpl       "Raw Parameter List" files.  Accompany raw format images or data cubes with the same name.  Contain information about the raw image, such as dimensions and data type.

• bmp      Windows bitmap       No encoding. 8 bit gray level, 8 bit indexed color, and 24 bit RGB.  2/1/08.  Also writes bmp files, pixmap data only - use TIF or RAW to record gray level image data of greater than 8-bits.                            
• dat      rae                  RAE image format.
  •                               Charles Evans - Resistive Anode Encoder
  •                               images. 1 and 2 unsigned bytes.
• dm2      dm2                  Digital Micrograph version 2. (Gatan Inc.)
• doc      not an image         Lets Lispix skip over .doc files when reading a folder of images.                            
• epm      NIST MAG EPM old     Old special NIST format for quantitated xray maps                           .
• epq      NIST MAG EPM         NIST format for quantitated xray maps.
  • Total x10 so that range is 0 - 1.0.
  • 5/01 DSB.  (Any image with "tot" in
  • the file name is multiplied by 10.  This is to compensate
  • for Bob M's quantitation code dividing the total map by 10.
  • Pixel values are mass fraction - range 0.0 - 1.0.
• gif      gif                  graphics interchange format.  Single image files.
• jpeg      jpg (PC) jpeg (Mac) Photographic Expert's Group.  Mac. Vanilla encoding schemes  
  • Note  Lispix does not read 'Exif' JPEG files - file commonly written by digital cameras.  As of 2/07, I read digital camera JPEG files with Photoshop6.0.1*  and write them back out from Photoshop as JPEG files using the Boxtop* Pro  JPEG 5.0.  Lispix reads these files.           
• ras      PGT RAS              Princeton Gamma Tech modification of raster file format.                            
• tif      TIF (PC), TIFF (Mac) Tagged image file format.  PC. 
  • Lispix does not read compressed files, such as LZW or FAX…
  • Lispix DOES read multiple image files, one image at a time.  9/8/03

    Data Cubes

• .raw  raw brick of bytes      single images or data cubes.  Needs the .rpl file.
• .ser  data cube
• .spd  data cube
• Notes on these three types

  Spectra

•  EDAX .spc file  See PPP Tool / Open / EDAX run, and File / File Utilities / Edax /

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Special image types:

Evans

16-bit RAE images, encoded in TIFF RGB format:  These images, would appear to be RGB TIFF images, and are interpreted by Photoshop, and Imagej that way.  However, the Evans RAE particle search software encodes bytes of these images as <R,G,B> = <???, HOB, LOB>.  Lispix detects these encoded images using these criteria:

•       TIFF tag 305 = "Kruwo so"     This is a special tag for the Evans images.
  •       256 x 256 pixels
  •       Photometric interpretation = 2 RGB color images.
  •       samples per pixel = 3.
If Lispix is set to open color images as gray level images, these images will be opened in their original form – 16 bit gray level images.  If Lispix is set to open color images as-is, these images will be opened as if they were RGB color images, and will probably look black or blue and banded.

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Notes on data cubes:

 

• ser     Emispec series file   Data cube format - recorded a spectrum at a time, one spectrum per pixel.
  • Format specified in 'MLx folder / data / image-file-formats / Emispec-ser-format.xls
  • / Emispec-tables.txt, which is read by Lispix in order  to read the .ser file.       
  • Tables describing the ser file format were obtained from: http://www.emispec.com/Support/Faq/SeriesFileFormat.html
  • mxl format note (Lispix does not read mxl files). 
• raw     raw file format       pixel data with no header.
  • If no .rpl file, use    'File / Import - Export Tool'
  • or, 'TOOLS / data cube / i/o / import from file' (which opens the import tool, which you then use).
• spd   Edax spectral data file format.  Similar to raw format, but with a small header that is copied to a .rpl file the first time the spd file is opened.

As of Lx132, raw and spd data cubes that are large are opened as file-based cubes.  Cropping channels and reducing the data types is no longer necessary.

As of Lx61, Lispix will automaticall re-save a data cube (in raw format, with m- appended to the front of the cube file and rpl file names) if it is able to use a reduced data type, such as byte or 16 bit, rather than, 32 bit.

For spectral images of 2048 channels only:  Lispix will give the option of cropping off the 1024 high energy channels in order to save memory.  If the cube is cropped, the cropped cube will be saved automatically, again with "m-" appended to the front of the file name.