Image Files that Lispix Reads

Contents || Index

11/09/2010

Files Lispix Reads

Allowed characters in file names. | Raw File Format

Lispix reads several types of images, data cubes, spectra and text .

(I have had problems analyzing data saved on network drives. If you have problems, move the images to your local hard drive.)

These are the file types that Lispix reads using the file menu:

Ascii

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.

Images

Common types

tif, tiff	Tagged image file format. 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
jpg, jpeg	Photographic Expert's Group. Some 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.
gif	Graphics interchange format. Single image files only.
bmp	Windows bitmap 8 bit gray level, 8 bit indexed color, and 24 bit RGB. No encoding. 2/1/08. Lispix writes bmp files with 8-bit pixmap data only. Use TIF or RAW to record gray level image data of greater than 8-bits.
raw	"Brick of bytes" - pixel image data without any dimensional or pixel depth information. Needs an accompanying .rpl file containing image dimensions, pixel type, etc.

Special Types

dm2	Digital Micrograph version 2. (Gatan Inc.*)
ras	Princeton Gamma Tech modification of raster file format
dat	Charles Evans* Resistive Anode Encoder, 1- or 2-byte images.
	Old Special Purpose NIST Formats
	Old Special Purpose NIST Formats
pix	512x512 single byte images
16b, 16x	16 bit unsigned. Usually 512x512.
epm	Quantitated x-ray maps saved as 16 bit integers.
epq	Quantitated x-ray maps saved as 16 bit integers. Atom percent values (0.0 - 100.0) interpreted as the pixel (integer) values divided by 100, Except the "TOT" or total image, where the values are divided by 10.

Data Cubes

Lispix opens spectrum images or data cubes of these types:

raw
"Brick of bytes" - pixel image data without any dimensional or pixel depth information. Needs an accompanying .rpl file containing cube dimensions, pixel type, etc.

ser
Notes

spd
Notes

(Lispix also opens data cubes as a folder of image files.)

Spectra

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

(Lispix does not do much with individual spectra.)

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.

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
- Documentation on the format (now labeled as TIA) as of 11/9/2010 is here: http://www.microscopy.cen.dtu.dk/~cbb/info/TIAformat/index.html
- Versions of Lispix after Lx170 (Nov. 2010) now also read 1-D ser files as a data cube one pixel high. These thin cubes might be thought of as the spectral version of intensity profiles, just as 2-D data cubes are spectral versions of images.
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.

Characters in file names:

Lispix file reader is not case sensitive.

Use these: A-Z or a-z, 0-9, -

Windows allows spaces, underscores and some other symbols. HTML files might not be found if they have spaces in their file names.

For moving files to other computer systems, avoid these: space, *, any punctuation character (except when part of a directory specification or as a wild card, or as a 'dot' before the extension).