Package gov.nih.mipav.model.file

Class FileLSM

java.lang.Object
gov.nih.mipav.model.file.FileBase
gov.nih.mipav.model.file.FileLSM
public class FileLSM extends FileBase
Reads Zeiss LSM 510 image files - an extension of the TIFF format. However, ordinary TIFF format supports both Little Endian(0x4949 or II) byte order and Big Endian (0x4d4d or MM) byte order. LSM supports only Little Endian byte order. NEW_SUBFILE_TYPE can be either 0 for images or 1 for thumbnails. The reader will skip over thumbnails and not include them in the read image. COMPRESSION can be either 1 for no compression or 5 for LZW compression.

One big difference between standard TIFF and the LSM format is the inclusion of the private CZ_LSMINFO tag. The pixel resolutions must be obtained from the VoxelSizeX, VoxelSizeY, and VoxelSizeZ fields in this private tag. This private tag appears only in the first image directory, so fileInfo.set operations must cycle thru all the slices using the values obtained when reading the first slice.

The x and y resolution units are always be in meters. LSM data may be 1, 2, or 3 channels. 1 data is black and white. Both 2 and 3 channels are RGB although in 2 channels only 2 of the 3 colors are used. LSM format uses either 8 bit unsigned data, 12 bit unsigned data, or 32 bit floats. Ths 12 bit unsigned data is stored in 16 bit shorts. If 2 or 3 channels use 12 bit unsigned data, then ARGB_USHORT format must be used, a format not found in ordinary TIFF. If a LSM file has 4 or more channels, then create another dimension in which to put each spectrum. The color map values are scaled to go only to 255.0 since a value of 65535 was observed in the unscaled map.

Ordinary TIFF uses the SAMPLE_FORMAT FIELD to specify how to interpret data with 1 = unsigned integer data, 2 = two's complement signed integer data, 3 = IEEE floating point data, and 4 = undefined data format. The default is 1, unsigned integer data. LSM files do not include the SAMPLE_FORMAT field, so if only TIFF rules were used the LSM 32 bit floating point numbers would be interpreted as unsigned integers.

The LSM release 6.0 documentation does not completely conform with the observed files. Table 16 with the CZ-Private tag shows a 488 byte structure, but at least some LSM files have values of 512 bytes in the s32StructureSize field. u32OffsetTimeStamps appears to point to a time stamps structure, but this structure contains the ascii such as Ch1-T1, Ch2-T2, and Ch3-T3 which does not appear in the table 22 structure for time stamp information. u32OffsetNextRecording appears to point to the start of a new structure, but it is not a second file header.

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  • Field Details

    • BYTE

      private static final int BYTE
      TIFF Types.
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    • ASCII

      private static final int ASCII
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    • SHORT

      private static final int SHORT
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    • LONG

      private static final int LONG
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    • RATIONAL

      private static final int RATIONAL
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    • SBYTE

      private static final int SBYTE
      2nd denom.
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    • UNDEFINED

      private static final int UNDEFINED
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    • SSHORT

      private static final int SSHORT
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    • SLONG

      private static final int SLONG
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    • SRATIONAL

      private static final int SRATIONAL
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    • FLOAT

      private static final int FLOAT
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    • DOUBLE

      private static final int DOUBLE
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    • NEW_SUBFILE_TYPE

      private static final int NEW_SUBFILE_TYPE
      TIFF Tags.
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    • IMAGE_WIDTH

      private static final int IMAGE_WIDTH
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    • IMAGE_LENGTH

      private static final int IMAGE_LENGTH
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    • BITS_PER_SAMPLE

      private static final int BITS_PER_SAMPLE
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    • COMPRESSION

      private static final int COMPRESSION
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    • PHOTO_INTERP

      private static final int PHOTO_INTERP
      3 = CCITT-T4, 4 = CCITT-T6, 5 = LZW, 32773 = packbits.
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    • IMAGE_DESCRIPTION

      private static final int IMAGE_DESCRIPTION
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    • STRIP_OFFSETS

      private static final int STRIP_OFFSETS
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    • SAMPLES_PER_PIXEL

      private static final int SAMPLES_PER_PIXEL
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    • ROWS_PER_STRIP

      private static final int ROWS_PER_STRIP
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    • STRIP_BYTE_COUNTS

      private static final int STRIP_BYTE_COUNTS
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    • MIN_SAMPLE_VALUE

      private static final int MIN_SAMPLE_VALUE
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    • MAX_SAMPLE_VALUE

      private static final int MAX_SAMPLE_VALUE
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    • XRESOLUTION

      private static final int XRESOLUTION
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    • YRESOLUTION

      private static final int YRESOLUTION
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    • PLANAR_CONFIG

      private static final int PLANAR_CONFIG
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    • RESOLUTION_UNIT

      private static final int RESOLUTION_UNIT
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    • SOFTWARE

      private static final int SOFTWARE
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    • DATE_TIME

      private static final int DATE_TIME
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    • PREDICTOR

      private static final int PREDICTOR
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    • COLOR_MAP

      private static final int COLOR_MAP
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    • TILE_WIDTH

      private static final int TILE_WIDTH
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    • TILE_LENGTH

      private static final int TILE_LENGTH
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    • TILE_OFFSETS

      private static final int TILE_OFFSETS
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    • TILE_BYTE_COUNTS

      private static final int TILE_BYTE_COUNTS
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    • SAMPLE_FORMAT

      private static final int SAMPLE_FORMAT
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    • CZ_LSMINFO

      private static final int CZ_LSMINFO
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    • SUBBLOCK_RECORDING

      private static final int SUBBLOCK_RECORDING
      Values for entries in scan information.
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    • SUBBLOCK_LASERS

      private static final int SUBBLOCK_LASERS
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    • SUBBLOCK_LASER

      private static final int SUBBLOCK_LASER
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    • SUBBLOCK_TRACKS

      private static final int SUBBLOCK_TRACKS
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    • SUBBLOCK_TRACK

      private static final int SUBBLOCK_TRACK
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    • SUBBLOCK_DETECTION_CHANNELS

      private static final int SUBBLOCK_DETECTION_CHANNELS
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    • SUBBLOCK_DETECTION_CHANNEL

      private static final int SUBBLOCK_DETECTION_CHANNEL
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    • SUBBLOCK_ILLUMINATION_CHANNELS

      private static final int SUBBLOCK_ILLUMINATION_CHANNELS
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    • SUBBLOCK_ILLUMINATION_CHANNEL

      private static final int SUBBLOCK_ILLUMINATION_CHANNEL
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    • SUBBLOCK_BEAM_SPLITTERS

      private static final int SUBBLOCK_BEAM_SPLITTERS
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    • SUBBLOCK_BEAM_SPLITTER

      private static final int SUBBLOCK_BEAM_SPLITTER
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    • SUBBLOCK_DATA_CHANNELS

      private static final int SUBBLOCK_DATA_CHANNELS
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    • SUBBLOCK_DATA_CHANNEL

      private static final int SUBBLOCK_DATA_CHANNEL
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    • SUBBLOCK_TIMERS

      private static final int SUBBLOCK_TIMERS
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    • SUBBLOCK_TIMER

      private static final int SUBBLOCK_TIMER
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    • SUBBLOCK_MARKERS

      private static final int SUBBLOCK_MARKERS
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    • SUBBLOCK_MARKER

      private static final int SUBBLOCK_MARKER
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    • SUBBLOCK_END

      private static final int SUBBLOCK_END
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    • RECORDING_ENTRY_NAME

      private static final int RECORDING_ENTRY_NAME
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    • RECORDING_ENTRY_DESCRIPTION

      private static final int RECORDING_ENTRY_DESCRIPTION
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    • RECORDING_ENTRY_NOTES

      private static final int RECORDING_ENTRY_NOTES
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    • RECORDING_ENTRY_OBJECTIVE

      private static final int RECORDING_ENTRY_OBJECTIVE
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    • RECORDING_ENTRY_PROCESSING_SUMMARY

      private static final int RECORDING_ENTRY_PROCESSING_SUMMARY
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    • RECORDING_ENTRY_SPECIAL_SCAN_MODE

      private static final int RECORDING_ENTRY_SPECIAL_SCAN_MODE
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    • RECORDING_ENTRY_SCAN_TYPE

      private static final int RECORDING_ENTRY_SCAN_TYPE
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    • OLEDB_RECORDING_ENTRY_SCAN_MODE

      private static final int OLEDB_RECORDING_ENTRY_SCAN_MODE
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    • RECORDING_ENTRY_NUMBER_OF_STACKS

      private static final int RECORDING_ENTRY_NUMBER_OF_STACKS
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    • RECORDING_ENTRY_LINES_PER_PLANE

      private static final int RECORDING_ENTRY_LINES_PER_PLANE
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    • RECORDING_ENTRY_SAMPLES_PER_LINE

      private static final int RECORDING_ENTRY_SAMPLES_PER_LINE
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    • RECORDING_ENTRY_PLANES_PER_VOLUME

      private static final int RECORDING_ENTRY_PLANES_PER_VOLUME
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    • RECORDING_ENTRY_IMAGES_WIDTH

      private static final int RECORDING_ENTRY_IMAGES_WIDTH
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    • RECORDING_ENTRY_IMAGES_HEIGHT

      private static final int RECORDING_ENTRY_IMAGES_HEIGHT
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    • RECORDING_ENTRY_IMAGES_NUMBER_PLANES

      private static final int RECORDING_ENTRY_IMAGES_NUMBER_PLANES
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    • RECORDING_ENTRY_IMAGES_NUMBER_STACKS

      private static final int RECORDING_ENTRY_IMAGES_NUMBER_STACKS
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    • RECORDING_ENTRY_IMAGES_NUMBER_CHANNELS

      private static final int RECORDING_ENTRY_IMAGES_NUMBER_CHANNELS
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    • RECORDING_ENTRY_LINSCAN_XY_SIZE

      private static final int RECORDING_ENTRY_LINSCAN_XY_SIZE
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    • RECORDING_ENTRY_SCAN_DIRECTION

      private static final int RECORDING_ENTRY_SCAN_DIRECTION
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    • RECORDING_ENTRY_TIME_SERIES

      private static final int RECORDING_ENTRY_TIME_SERIES
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    • RECORDING_ENTRY_ORIGINAL_SCAN_DATA

      private static final int RECORDING_ENTRY_ORIGINAL_SCAN_DATA
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    • RECORDING_ENTRY_ZOOM_X

      private static final int RECORDING_ENTRY_ZOOM_X
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    • RECORDING_ENTRY_ZOOM_Y

      private static final int RECORDING_ENTRY_ZOOM_Y
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    • RECORDING_ENTRY_ZOOM_Z

      private static final int RECORDING_ENTRY_ZOOM_Z
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    • RECORDING_ENTRY_SAMPLE_0X

      private static final int RECORDING_ENTRY_SAMPLE_0X
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    • RECORDING_ENTRY_SAMPLE_0Y

      private static final int RECORDING_ENTRY_SAMPLE_0Y
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    • RECORDING_ENTRY_SAMPLE_0Z

      private static final int RECORDING_ENTRY_SAMPLE_0Z
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    • RECORDING_ENTRY_SAMPLE_SPACING

      private static final int RECORDING_ENTRY_SAMPLE_SPACING
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    • RECORDING_ENTRY_LINE_SPACING

      private static final int RECORDING_ENTRY_LINE_SPACING
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    • RECORDING_ENTRY_PLANE_SPACING

      private static final int RECORDING_ENTRY_PLANE_SPACING
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    • RECORDING_ENTRY_PLANE_WIDTH

      private static final int RECORDING_ENTRY_PLANE_WIDTH
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    • RECORDING_ENTRY_PLANE_HEIGHT

      private static final int RECORDING_ENTRY_PLANE_HEIGHT
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    • RECORDING_ENTRY_VOLUME_DEPTH

      private static final int RECORDING_ENTRY_VOLUME_DEPTH
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    • RECORDING_ENTRY_ROTATION

      private static final int RECORDING_ENTRY_ROTATION
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    • RECORDING_ENTRY_NUTATION

      private static final int RECORDING_ENTRY_NUTATION
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    • RECORDING_ENTRY_PRECESSION

      private static final int RECORDING_ENTRY_PRECESSION
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    • RECORDING_ENTRY_SAMPLE_0TIME

      private static final int RECORDING_ENTRY_SAMPLE_0TIME
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    • RECORDING_ENTRY_START_SCAN_TRIGGER_IN

      private static final int RECORDING_ENTRY_START_SCAN_TRIGGER_IN
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    • RECORDING_ENTRY_START_SCAN_TRIGGER_OUT

      private static final int RECORDING_ENTRY_START_SCAN_TRIGGER_OUT
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    • RECORDING_ENTRY_START_SCAN_EVENT

      private static final int RECORDING_ENTRY_START_SCAN_EVENT
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    • RECORDING_ENTRY_START_SCAN_TIME

      private static final int RECORDING_ENTRY_START_SCAN_TIME
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    • RECORDING_ENTRY_STOP_SCAN_TRIGGER_IN

      private static final int RECORDING_ENTRY_STOP_SCAN_TRIGGER_IN
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    • RECORDING_ENTRY_STOP_SCAN_TRIGGER_OUT

      private static final int RECORDING_ENTRY_STOP_SCAN_TRIGGER_OUT
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    • RECORDING_ENTRY_STOP_SCAN_EVENT

      private static final int RECORDING_ENTRY_STOP_SCAN_EVENT
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    • RECORDING_ENTRY_STOP_SCAN_TIME

      private static final int RECORDING_ENTRY_STOP_SCAN_TIME
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    • RECORDING_ENTRY_USE_ROIS

      private static final int RECORDING_ENTRY_USE_ROIS
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    • RECORDING_ENTRY_USE_REDUCED_MEMORY_ROIS

      private static final int RECORDING_ENTRY_USE_REDUCED_MEMORY_ROIS
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    • RECORDING_ENTRY_USER

      private static final int RECORDING_ENTRY_USER
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    • RECORDING_ENTRY_USE_BCCORRECTION

      private static final int RECORDING_ENTRY_USE_BCCORRECTION
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    • RECORDING_ENTRY_POSITION_BCCORRECTION1

      private static final int RECORDING_ENTRY_POSITION_BCCORRECTION1
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    • RECORDING_ENTRY_POSITION_BCCORRECTION2

      private static final int RECORDING_ENTRY_POSITION_BCCORRECTION2
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    • RECORDING_ENTRY_INTERPOLATIONY

      private static final int RECORDING_ENTRY_INTERPOLATIONY
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    • RECORDING_ENTRY_CAMERA_BINNING

      private static final int RECORDING_ENTRY_CAMERA_BINNING
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    • RECORDING_ENTRY_CAMERA_SUPERSAMPLING

      private static final int RECORDING_ENTRY_CAMERA_SUPERSAMPLING
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    • RECORDING_ENTRY_CAMERA_FRAME_WIDTH

      private static final int RECORDING_ENTRY_CAMERA_FRAME_WIDTH
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    • RECORDING_ENTRY_CAMERA_FRAME_HEIGHT

      private static final int RECORDING_ENTRY_CAMERA_FRAME_HEIGHT
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    • RECORDING_ENTRY_CAMERA_OFFSETX

      private static final int RECORDING_ENTRY_CAMERA_OFFSETX
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    • RECORDING_ENTRY_CAMERA_OFFSETY

      private static final int RECORDING_ENTRY_CAMERA_OFFSETY
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    • RECORDING_ENTRY_RT_BINNING

      private static final int RECORDING_ENTRY_RT_BINNING
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    • RECORDING_ENTRY_RT_FRAME_WIDTH

      private static final int RECORDING_ENTRY_RT_FRAME_WIDTH
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    • RECORDING_ENTRY_RT_FRAME_HEIGHT

      private static final int RECORDING_ENTRY_RT_FRAME_HEIGHT
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    • RECORDING_ENTRY_RT_REGION_WIDTH

      private static final int RECORDING_ENTRY_RT_REGION_WIDTH
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    • RECORDING_ENTRY_RT_REGION_HEIGHT

      private static final int RECORDING_ENTRY_RT_REGION_HEIGHT
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    • RECORDING_ENTRY_RT_OFFSETX

      private static final int RECORDING_ENTRY_RT_OFFSETX
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    • RECORDING_ENTRY_RT_OFFSETY

      private static final int RECORDING_ENTRY_RT_OFFSETY
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    • RECORDING_ENTRY_RT_ZOOM

      private static final int RECORDING_ENTRY_RT_ZOOM
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    • RECORDING_ENTRY_RT_LINEPERIOD

      private static final int RECORDING_ENTRY_RT_LINEPERIOD
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    • RECORDING_ENTRY_PRESCAN

      private static final int RECORDING_ENTRY_PRESCAN
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    • RECORDING_ENTRY_SCAN_DIRECTIONZ

      private static final int RECORDING_ENTRY_SCAN_DIRECTIONZ
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    • TRACK_ENTRY_MULTIPLEX_TYPE

      private static final int TRACK_ENTRY_MULTIPLEX_TYPE
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    • TRACK_ENTRY_MULTIPLEX_ORDER

      private static final int TRACK_ENTRY_MULTIPLEX_ORDER
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    • TRACK_ENTRY_SAMPLING_MODE

      private static final int TRACK_ENTRY_SAMPLING_MODE
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    • TRACK_ENTRY_SAMPLING_METHOD

      private static final int TRACK_ENTRY_SAMPLING_METHOD
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    • TRACK_ENTRY_SAMPLING_NUMBER

      private static final int TRACK_ENTRY_SAMPLING_NUMBER
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    • TRACK_ENTRY_ACQUIRE

      private static final int TRACK_ENTRY_ACQUIRE
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    • TRACK_ENTRY_SAMPLE_OBSERVATION_TIME

      private static final int TRACK_ENTRY_SAMPLE_OBSERVATION_TIME
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    • TRACK_ENTRY_TIME_BETWEEN_STACKS

      private static final int TRACK_ENTRY_TIME_BETWEEN_STACKS
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    • TRACK_ENTRY_NAME

      private static final int TRACK_ENTRY_NAME
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    • TRACK_ENTRY_COLLIMATOR1_NAME

      private static final int TRACK_ENTRY_COLLIMATOR1_NAME
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    • TRACK_ENTRY_COLLIMATOR1_POSITION

      private static final int TRACK_ENTRY_COLLIMATOR1_POSITION
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    • TRACK_ENTRY_COLLIMATOR2_NAME

      private static final int TRACK_ENTRY_COLLIMATOR2_NAME
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    • TRACK_ENTRY_COLLIMATOR2_POSITION

      private static final int TRACK_ENTRY_COLLIMATOR2_POSITION
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    • TRACK_ENTRY_IS_BLEACH_TRACK

      private static final int TRACK_ENTRY_IS_BLEACH_TRACK
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    • TRACK_ENTRY_IS_BLEACH_AFTER_SCAN_NUMBER

      private static final int TRACK_ENTRY_IS_BLEACH_AFTER_SCAN_NUMBER
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    • TRACK_ENTRY_BLEACH_SCAN_NUMBER

      private static final int TRACK_ENTRY_BLEACH_SCAN_NUMBER
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    • TRACK_ENTRY_TRIGGER_IN

      private static final int TRACK_ENTRY_TRIGGER_IN
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    • TRACK_ENTRY_TRIGGER_OUT

      private static final int TRACK_ENTRY_TRIGGER_OUT
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    • TRACK_ENTRY_IS_RATIO_TRACK

      private static final int TRACK_ENTRY_IS_RATIO_TRACK
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    • TRACK_ENTRY_BLEACH_COUNT

      private static final int TRACK_ENTRY_BLEACH_COUNT
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    • TRACK_ENTRY_SPI_CENTER_WAVELENGTH

      private static final int TRACK_ENTRY_SPI_CENTER_WAVELENGTH
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    • TRACK_ENTRY_PIXEL_TIME

      private static final int TRACK_ENTRY_PIXEL_TIME
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    • TRACK_ENTRY_ID_CONDENSOR_FRONTLENS

      private static final int TRACK_ENTRY_ID_CONDENSOR_FRONTLENS
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    • TRACK_ENTRY_CONDENSOR_FRONTLENS

      private static final int TRACK_ENTRY_CONDENSOR_FRONTLENS
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    • TRACK_ENTRY_ID_FIELD_STOP

      private static final int TRACK_ENTRY_ID_FIELD_STOP
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    • TRACK_ENTRY_FIELD_STOP_VALUE

      private static final int TRACK_ENTRY_FIELD_STOP_VALUE
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    • TRACK_ENTRY_ID_CONDENSOR_APERTURE

      private static final int TRACK_ENTRY_ID_CONDENSOR_APERTURE
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    • TRACK_ENTRY_CONDENSOR_APERTURE

      private static final int TRACK_ENTRY_CONDENSOR_APERTURE
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    • TRACK_ENTRY_ID_CONDENSOR_REVOLVER

      private static final int TRACK_ENTRY_ID_CONDENSOR_REVOLVER
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    • TRACK_ENTRY_CONDENSOR_FILTER

      private static final int TRACK_ENTRY_CONDENSOR_FILTER
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    • TRACK_ENTRY_ID_TRANSMISSION_FILTER1

      private static final int TRACK_ENTRY_ID_TRANSMISSION_FILTER1
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    • TRACK_ENTRY_ID_TRANSMISSION1

      private static final int TRACK_ENTRY_ID_TRANSMISSION1
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    • TRACK_ENTRY_ID_TRANSMISSION_FILTER2

      private static final int TRACK_ENTRY_ID_TRANSMISSION_FILTER2
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    • TRACK_ENTRY_ID_TRANSMISSION2

      private static final int TRACK_ENTRY_ID_TRANSMISSION2
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    • TRACK_ENTRY_REPEAT_BLEACH

      private static final int TRACK_ENTRY_REPEAT_BLEACH
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    • TRACK_ENTRY_ENABLE_SPOT_BLEACH_POS

      private static final int TRACK_ENTRY_ENABLE_SPOT_BLEACH_POS
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    • TRACK_ENTRY_SPOT_BLEACH_POSX

      private static final int TRACK_ENTRY_SPOT_BLEACH_POSX
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    • TRACK_ENTRY_SPOT_BLEACH_POSY

      private static final int TRACK_ENTRY_SPOT_BLEACH_POSY
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    • TRACK_ENTRY_BLEACH_POSITION_Z

      private static final int TRACK_ENTRY_BLEACH_POSITION_Z
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    • TRACK_ENTRY_ID_TUBELENS

      private static final int TRACK_ENTRY_ID_TUBELENS
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    • TRACK_ENTRY_ID_TUBELENS_POSITION

      private static final int TRACK_ENTRY_ID_TUBELENS_POSITION
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    • TRACK_TRANSMITTED_LIGHT

      private static final int TRACK_TRANSMITTED_LIGHT
      See Also:

    • TRACK_REFLECTED_LIGHT

      private static final int TRACK_REFLECTED_LIGHT
      See Also:

    • TRACK_SIMULTAN_GRAB_AND_BLEACH

      private static final int TRACK_SIMULTAN_GRAB_AND_BLEACH
      See Also:

    • TRACK_BLEACH_PIXEL_TIME

      private static final int TRACK_BLEACH_PIXEL_TIME
      See Also:

    • LASER_ENTRY_NAME

      private static final int LASER_ENTRY_NAME
      DOCUMENT ME!
      See Also:

    • LASER_ENTRY_ACQUIRE

      private static final int LASER_ENTRY_ACQUIRE
      DOCUMENT ME!
      See Also:

    • LASER_ENTRY_POWER

      private static final int LASER_ENTRY_POWER
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_INTEGRATION_MODE

      private static final int DETCHANNEL_ENTRY_INTEGRATION_MODE
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_SPECIAL_MODE

      private static final int DETCHANNEL_ENTRY_SPECIAL_MODE
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_DETECTOR_GAIN_FIRST

      private static final int DETCHANNEL_ENTRY_DETECTOR_GAIN_FIRST
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_DETECTOR_GAIN_LAST

      private static final int DETCHANNEL_ENTRY_DETECTOR_GAIN_LAST
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_AMPLIFIER_GAIN_FIRST

      private static final int DETCHANNEL_ENTRY_AMPLIFIER_GAIN_FIRST
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_AMPLIFIER_GAIN_LAST

      private static final int DETCHANNEL_ENTRY_AMPLIFIER_GAIN_LAST
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_AMPLIFIER_OFFS_FIRST

      private static final int DETCHANNEL_ENTRY_AMPLIFIER_OFFS_FIRST
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_AMPLIFIER_OFFS_LAST

      private static final int DETCHANNEL_ENTRY_AMPLIFIER_OFFS_LAST
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_PINHOLE_DIAMETER

      private static final int DETCHANNEL_ENTRY_PINHOLE_DIAMETER
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_COUNTING_TRIGGER

      private static final int DETCHANNEL_ENTRY_COUNTING_TRIGGER
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_ENTRY_ACQUIRE

      private static final int DETCHANNEL_ENTRY_ACQUIRE
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_POINT_DETECTOR_NAME

      private static final int DETCHANNEL_POINT_DETECTOR_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_AMPLIFIER_NAME

      private static final int DETCHANNEL_AMPLIFIER_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_PINHOLE_NAME

      private static final int DETCHANNEL_PINHOLE_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_FILTER_SET_NAME

      private static final int DETCHANNEL_FILTER_SET_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_FILTER_NAME

      private static final int DETCHANNEL_FILTER_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_INTEGRATOR_NAME

      private static final int DETCHANNEL_INTEGRATOR_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_DETECTION_CHANNEL_NAME

      private static final int DETCHANNEL_DETECTION_CHANNEL_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_DETECTOR_GAIN_BC1

      private static final int DETCHANNEL_DETECTOR_GAIN_BC1
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_DETECTOR_GAIN_BC2

      private static final int DETCHANNEL_DETECTOR_GAIN_BC2
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_AMPLIFIER_GAIN_BC1

      private static final int DETCHANNEL_AMPLIFIER_GAIN_BC1
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_AMPLIFIER_GAIN_BC2

      private static final int DETCHANNEL_AMPLIFIER_GAIN_BC2
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_AMPLIFIER_OFFSET_BC1

      private static final int DETCHANNEL_AMPLIFIER_OFFSET_BC1
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_AMPLIFIER_OFFSET_BC2

      private static final int DETCHANNEL_AMPLIFIER_OFFSET_BC2
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_SPECTRAL_SCAN_CHANNELS

      private static final int DETCHANNEL_SPECTRAL_SCAN_CHANNELS
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_SPI_WAVELENGTH_START

      private static final int DETCHANNEL_SPI_WAVELENGTH_START
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_SPI_WAVELENGTH_END

      private static final int DETCHANNEL_SPI_WAVELENGTH_END
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_DYE_NAME

      private static final int DETCHANNEL_DYE_NAME
      DOCUMENT ME!
      See Also:

    • DETCHANNEL_DYE_FOLDER

      private static final int DETCHANNEL_DYE_FOLDER
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_ENTRY_NAME

      private static final int ILLUMCHANNEL_ENTRY_NAME
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_ENTRY_POWER

      private static final int ILLUMCHANNEL_ENTRY_POWER
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_ENTRY_WAVELENGTH

      private static final int ILLUMCHANNEL_ENTRY_WAVELENGTH
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_ENTRY_ACQUIRE

      private static final int ILLUMCHANNEL_ENTRY_ACQUIRE
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_DETCHANNEL_NAME

      private static final int ILLUMCHANNEL_DETCHANNEL_NAME
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_POWER_BC1

      private static final int ILLUMCHANNEL_POWER_BC1
      DOCUMENT ME!
      See Also:

    • ILLUMCHANNEL_POWER_BC2

      private static final int ILLUMCHANNEL_POWER_BC2
      DOCUMENT ME!
      See Also:

    • BEAMSPLITTER_ENTRY_FILTER_SET

      private static final int BEAMSPLITTER_ENTRY_FILTER_SET
      DOCUMENT ME!
      See Also:

    • BEAMSPLITTER_ENTRY_FILTER

      private static final int BEAMSPLITTER_ENTRY_FILTER
      DOCUMENT ME!
      See Also:

    • BEAMSPLITTER_ENTRY_NAME

      private static final int BEAMSPLITTER_ENTRY_NAME
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_NAME

      private static final int DATACHANNEL_ENTRY_NAME
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_COLOR

      private static final int DATACHANNEL_ENTRY_COLOR
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_SAMPLETYPE

      private static final int DATACHANNEL_ENTRY_SAMPLETYPE
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_BITSPERSAMPLE

      private static final int DATACHANNEL_ENTRY_BITSPERSAMPLE
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_TYPE

      private static final int DATACHANNEL_ENTRY_RATIO_TYPE
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_TRACK1

      private static final int DATACHANNEL_ENTRY_RATIO_TRACK1
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_TRACK2

      private static final int DATACHANNEL_ENTRY_RATIO_TRACK2
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CHANNEL1

      private static final int DATACHANNEL_ENTRY_RATIO_CHANNEL1
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CHANNEL2

      private static final int DATACHANNEL_ENTRY_RATIO_CHANNEL2
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CONST1

      private static final int DATACHANNEL_ENTRY_RATIO_CONST1
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CONST2

      private static final int DATACHANNEL_ENTRY_RATIO_CONST2
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CONST3

      private static final int DATACHANNEL_ENTRY_RATIO_CONST3
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CONST4

      private static final int DATACHANNEL_ENTRY_RATIO_CONST4
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CONST5

      private static final int DATACHANNEL_ENTRY_RATIO_CONST5
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_CONST6

      private static final int DATACHANNEL_ENTRY_RATIO_CONST6
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_FIRST_IMAGES1

      private static final int DATACHANNEL_ENTRY_RATIO_FIRST_IMAGES1
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_RATIO_FIRST_IMAGES2

      private static final int DATACHANNEL_ENTRY_RATIO_FIRST_IMAGES2
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_DYE_NAME

      private static final int DATACHANNEL_ENTRY_DYE_NAME
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_DYE_FOLDER

      private static final int DATACHANNEL_ENTRY_DYE_FOLDER
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_SPECTRUM

      private static final int DATACHANNEL_ENTRY_SPECTRUM
      DOCUMENT ME!
      See Also:

    • DATACHANNEL_ENTRY_ACQUIRE

      private static final int DATACHANNEL_ENTRY_ACQUIRE
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_NAME

      private static final int TIMER_ENTRY_NAME
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_DESCRIPTION

      private static final int TIMER_ENTRY_DESCRIPTION
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_INTERVAL

      private static final int TIMER_ENTRY_INTERVAL
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_TRIGGER_IN

      private static final int TIMER_ENTRY_TRIGGER_IN
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_TRIGGER_OUT

      private static final int TIMER_ENTRY_TRIGGER_OUT
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_ACTIVATION_TIME

      private static final int TIMER_ENTRY_ACTIVATION_TIME
      DOCUMENT ME!
      See Also:

    • TIMER_ENTRY_ACTIVATION_NUMBER

      private static final int TIMER_ENTRY_ACTIVATION_NUMBER
      DOCUMENT ME!
      See Also:

    • MARKER_ENTRY_NAME

      private static final int MARKER_ENTRY_NAME
      DOCUMENT ME!
      See Also:

    • MARKER_ENTRY_DESCRIPTION

      private static final int MARKER_ENTRY_DESCRIPTION
      DOCUMENT ME!
      See Also:

    • MARKER_ENTRY_TRIGGER_IN

      private static final int MARKER_ENTRY_TRIGGER_IN
      DOCUMENT ME!
      See Also:

    • MARKER_ENTRY_TRIGGER_OUT

      private static final int MARKER_ENTRY_TRIGGER_OUT
      DOCUMENT ME!
      See Also:

    • TYPE_SUBBLOCK

      private static final int TYPE_SUBBLOCK
      Values for types in scan information.
      See Also:

    • TYPE_LONG

      private static final int TYPE_LONG
      DOCUMENT ME!
      See Also:

    • TYPE_RATIONAL

      private static final int TYPE_RATIONAL
      DOCUMENT ME!
      See Also:

    • TYPE_ASCII

      private static final int TYPE_ASCII
      DOCUMENT ME!
      See Also:

    • RECTANGLE

      private static final int RECTANGLE
      Bleached ROI shapes.
      See Also:

    • ELLIPSE

      private static final int ELLIPSE
      DOCUMENT ME!
      See Also:

    • CLOSED_POLYLINE

      private static final int CLOSED_POLYLINE
      DOCUMENT ME!
      See Also:

    • CLOSED_BEZIER

      private static final int CLOSED_BEZIER
      DOCUMENT ME!
      See Also:

    • CIRCLE

      private static final int CIRCLE
      DOCUMENT ME!
      See Also:

    • VECTOR_OVERLAY

      private static final int VECTOR_OVERLAY
      Types of drawing elements.
      See Also:

    • ROI

      private static final int ROI
      DOCUMENT ME!
      See Also:

    • BLEACH_ROI

      private static final int BLEACH_ROI
      DOCUMENT ME!
      See Also:

    • MEANOFROIS_OVERLAY

      private static final int MEANOFROIS_OVERLAY
      DOCUMENT ME!
      See Also:

    • TOPOLSOLINE_OVERLAY

      private static final int TOPOLSOLINE_OVERLAY
      DOCUMENT ME!
      See Also:

    • TOPOPROFILE_OVERLAY

      private static final int TOPOPROFILE_OVERLAY
      DOCUMENT ME!
      See Also:

    • LINESCAN_OVERLAY

      private static final int LINESCAN_OVERLAY
      DOCUMENT ME!
      See Also:

    • INPUT_LUT

      private static final int INPUT_LUT
      Types of LUTS.
      See Also:

    • OUTPUT_LUT

      private static final int OUTPUT_LUT
      DOCUMENT ME!
      See Also:

    • ZRESOLUTION

      private static final int ZRESOLUTION
      EchoTech Tiff TAGS.
      See Also:

    • TRESOLUTION

      private static final int TRESOLUTION
      DOCUMENT ME!
      See Also:

    • bleachedROIShape

      private int bleachedROIShape
      DOCUMENT ME!

    • bleachKnotX

      private double[] bleachKnotX
      DOCUMENT ME!

    • bleachKnotY

      private double[] bleachKnotY
      DOCUMENT ME!

    • blueArray

      private int[] blueArray
      DOCUMENT ME!

    • blueOffset

      private int blueOffset
      DOCUMENT ME!

    • byteBuffer

      private byte[] byteBuffer
      DOCUMENT ME!

    • channelDataTypes

      private int[] channelDataTypes
      DOCUMENT ME!

    • channelNames

      private String[] channelNames
      DOCUMENT ME!

    • chunky

      private boolean chunky
      DOCUMENT ME!

    • czChannels

      private int czChannels
      DOCUMENT ME!

    • czDataType

      private int czDataType
      DOCUMENT ME!

    • czDataType2

      private int czDataType2
      DOCUMENT ME!

    • czDimT

      private int czDimT
      DOCUMENT ME!

    • czDimX

      private int czDimX
      DOCUMENT ME!

    • czDimY

      private int czDimY
      DOCUMENT ME!

    • czDimZ

      private int czDimZ
      DOCUMENT ME!

    • czScanType

      private int czScanType
      DOCUMENT ME!

    • czSpectralScan

      private int czSpectralScan
      DOCUMENT ME!

    • dataOffsets

      private Vector<FileLSM.Index>[] dataOffsets

    • dateTime

      private byte[] dateTime
      DOCUMENT ME!

    • decomp

      private byte[] decomp
      DOCUMENT ME!

    • dimensionM

      private int dimensionM

    • dimensionP

      private int dimensionP

    • dimensionsReserved

      private int[] dimensionsReserved

    • displayAspectTime

      private double displayAspectTime
      DOCUMENT ME!

    • displayAspectX

      private double displayAspectX
      DOCUMENT ME!

    • displayAspectY

      private double displayAspectY
      DOCUMENT ME!

    • displayAspectZ

      private double displayAspectZ
      DOCUMENT ME!

    • doTile

      private boolean doTile
      DOCUMENT ME!

    • drawingElement

      private int drawingElement
      DOCUMENT ME!

    • endianess

      private boolean endianess
      DOCUMENT ME!

    • eventDescription

      private String[] eventDescription
      DOCUMENT ME!

    • eventTime

      private double[] eventTime
      DOCUMENT ME!

    • eventType

      private int[] eventType
      DOCUMENT ME!

    • file

      private File file
      DOCUMENT ME!

    • fileDataType

      private int fileDataType
      DOCUMENT ME!

    • fileDir

      private String fileDir
      DOCUMENT ME!

    • fileInfo

      private FileInfoLSM fileInfo
      DOCUMENT ME!

    • fileName

      private String fileName
      DOCUMENT ME!

    • firstSliceAfterBleach

      private int firstSliceAfterBleach
      DOCUMENT ME!

    • greenArray

      private int[] greenArray
      DOCUMENT ME!

    • greenOffset

      private int greenOffset
      DOCUMENT ME!

    • haveBleachedBezier

      private boolean haveBleachedBezier
      DOCUMENT ME!

    • haveBleachedCircle

      private boolean haveBleachedCircle
      DOCUMENT ME!

    • haveBleachedCirclePerim3

      private boolean haveBleachedCirclePerim3
      DOCUMENT ME!

    • haveBleachedEllipse

      private boolean haveBleachedEllipse
      DOCUMENT ME!

    • haveBleachedPolyline

      private boolean haveBleachedPolyline
      DOCUMENT ME!

    • haveBleachedRectangle

      private boolean haveBleachedRectangle
      DOCUMENT ME!

    • IFDoffsets

      private int[] IFDoffsets
      DOCUMENT ME!

    • image

      private ModelImage image
      DOCUMENT ME!

    • imageDescription

      private byte[] imageDescription
      DOCUMENT ME!

    • imageSlice

      private int imageSlice
      DOCUMENT ME!

    • img3DMultiBuffer

      private float[][] img3DMultiBuffer
      DOCUMENT ME!

    • imgBuffer

      private float[] imgBuffer
      DOCUMENT ME!

    • imgResols

      private float[] imgResols
      DOCUMENT ME!

    • internalUse1

      private int internalUse1

    • knotX

      private double[] knotX
      DOCUMENT ME!

    • knotY

      private double[] knotY
      DOCUMENT ME!

    • lastSliceBeforeBleach

      private int lastSliceBeforeBleach
      DOCUMENT ME!

    • LUT

      private ModelLUT LUT
      DOCUMENT ME!

    • lutKind

      private int lutKind
      DOCUMENT ME!

    • lzwCompression

      private boolean lzwCompression
      DOCUMENT ME!

    • lzwDecoder

      private TIFFLZWDecoder lzwDecoder
      DOCUMENT ME!

    • manySpectrums

      private boolean manySpectrums
      DOCUMENT ME!

    • mono

      private int mono
      DOCUMENT ME!

    • numberColors

      private int numberColors
      DOCUMENT ME!

    • objectiveSphereCorrection

      private double objectiveSphereCorrection
      DOCUMENT ME!

    • offsetAcquisitionParameters

      private int offsetAcquisitionParameters

    • offsetBleachRoi

      private int offsetBleachRoi
      DOCUMENT ME!

    • offsetChannelColors

      private int offsetChannelColors
      DOCUMENT ME!

    • offsetChannelDataTypes

      private int offsetChannelDataTypes
      DOCUMENT ME!

    • offsetChannelFactors

      private int offsetChannelFactors
      DOCUMENT ME!

    • offsetChannelWavelength

      private int offsetChannelWavelength
      DOCUMENT ME!

    • offsetCharacteristics

      private int offsetCharacteristics

    • offsetEventList

      private int offsetEventList
      DOCUMENT ME!

    • offsetInputLut

      private int offsetInputLut
      DOCUMENT ME!

    • offsetKsData

      private int offsetKsData
      DOCUMENT ME!

    • offsetLinescanOverlay

      private int offsetLinescanOverlay
      DOCUMENT ME!

    • offsetMeanOfRoisOverlay

      private int offsetMeanOfRoisOverlay
      DOCUMENT ME!

    • offsetOutputLut

      private int offsetOutputLut
      DOCUMENT ME!

    • offsetRoi

      private int offsetRoi
      DOCUMENT ME!

    • offsetPalette

      private int offsetPalette

    • offsetPositions

      private int offsetPositions

    • offsetScanInformation

      private int offsetScanInformation
      DOCUMENT ME!

    • offsetTilePositions

      private int offsetTilePositions

    • offsetTimeStamps

      private int offsetTimeStamps
      DOCUMENT ME!

    • offsetTopolsolineOverlay

      private int offsetTopolsolineOverlay
      DOCUMENT ME!

    • offsetTopoProfileOverlay

      private int offsetTopoProfileOverlay
      DOCUMENT ME!

    • offsetUnmixParameters

      private int offsetUnmixParameters
      DOCUMENT ME!

    • offsetVectorOverlay

      private int offsetVectorOverlay
      DOCUMENT ME!

    • originX

      private double originX
      The x-offset of the center of the image in meter relative to the optical axis. For LSM images the x-direction is the direction of the x-scanner. In releases prior to 4.0 the entry was not used and the value 0 was written instead.

    • originY

      private double originY
      The y-offset of the center of the image in meter relative to the optical axis. For LSM images the y-direction is the direction of the y-scanner. In releases prior to 4.0 the entry was not used and the value 0 was written instead.

    • packBit

      private boolean packBit
      DOCUMENT ME!

    • photoBleachedVOI

      private VOI photoBleachedVOI
      DOCUMENT ME!

    • predictor

      private int predictor
      DOCUMENT ME!

    • redArray

      private int[] redArray
      DOCUMENT ME!

    • redOffset

      private int redOffset
      Default ordering is red, green, blue.

    • reserved

      private int[] reserved

    • rowsPerStrip

      private int rowsPerStrip
      DOCUMENT ME!

    • samplesPerPixel

      private int samplesPerPixel
      private short nDirEntries;.

    • secondAddress

      private int secondAddress
      DOCUMENT ME!

    • secondImage

      private int secondImage
      DOCUMENT ME!

    • software

      private byte[] software
      DOCUMENT ME!

    • spectrumNumber

      private int spectrumNumber
      DOCUMENT ME!

    • str

      private String str
      DOCUMENT ME!

    • thumbNail

      private boolean thumbNail
      DOCUMENT ME!

    • thumbnailOffset

      private long thumbnailOffset
      DOCUMENT ME!

    • thumbNailX

      private int thumbNailX
      DOCUMENT ME!

    • thumbNailY

      private int thumbNailY
      DOCUMENT ME!

    • tileByteCounts

      private int[] tileByteCounts
      DOCUMENT ME!

    • tileByteNumber

      private int tileByteNumber
      DOCUMENT ME!

    • tileLength

      private int tileLength
      DOCUMENT ME!

    • tileMaxByteCount

      private int tileMaxByteCount
      DOCUMENT ME!

    • tileOffsetNumber

      private int tileOffsetNumber
      DOCUMENT ME!

    • tileOffsets

      private long[] tileOffsets
      DOCUMENT ME!

    • tilesAcross

      private int tilesAcross
      DOCUMENT ME!

    • tilesDown

      private int tilesDown
      DOCUMENT ME!

    • tilesPerImage

      private int tilesPerImage
      DOCUMENT ME!

    • tilesPerSlice

      private int tilesPerSlice
      DOCUMENT ME!

    • tileTemp

      private long[] tileTemp
      DOCUMENT ME!

    • tileWidth

      private int tileWidth
      DOCUMENT ME!

    • timeDifferenceX

      private double timeDifferenceX

    • timeDifferenceY

      private double timeDifferenceY

    • timeDifferenceZ

      private double timeDifferenceZ

    • timeInterval

      private double timeInterval
      DOCUMENT ME!

    • timeStamp

      private double[] timeStamp
      DOCUMENT ME!

    • toolbarFlags

      private int toolbarFlags
      DOCUMENT ME!

    • UI

      private ViewUserInterface UI
      DOCUMENT ME!

    • unitsOfMeasure

      private int[] unitsOfMeasure
      DOCUMENT ME!

    • voxelSizeX

      private double voxelSizeX
      DOCUMENT ME!

    • voxelSizeY

      private double voxelSizeY
      DOCUMENT ME!

    • voxelSizeZ

      private double voxelSizeZ
      DOCUMENT ME!

    • wavelengthNumber

      private int wavelengthNumber
      DOCUMENT ME!

    • wavelengths

      private double[] wavelengths
      DOCUMENT ME!

    • xDim

      private int xDim
      DOCUMENT ME!

    • yDim

      private int yDim
      DOCUMENT ME!

    • zDim

      private int zDim
      DOCUMENT ME!

  • Constructor Details

    • FileLSM

      public FileLSM(String fileName, String fileDir, int secondAddress) throws IOException
      LSM reader/writer constructor.
      Parameters:
      fileName - file name
      fileDir - file directory
      secondAddress - the position within the image file to begin reading from
      Throws:
      IOException - if there is an error making the file

  • Method Details

    • finalize

      public void finalize()
      Prepares this class for cleanup. Calls the finalize method for existing elements, closes any open files and sets other elements to null.
      Overrides:
      finalize in class FileBase

    • getFileInfo

      public FileInfoBase getFileInfo()
      Accessor that returns the file info.
      Returns:
      FileInfoBase containing the file info

    • getImage3DMultiBuffer

      public float[][] getImage3DMultiBuffer()
      Accessor that returns the image buffer.
      Returns:
      buffer of image.

    • getImageBuffer

      public float[] getImageBuffer()
      Accessor that returns the image buffer.
      Returns:
      buffer of image.

    • getModelLUT

      public ModelLUT getModelLUT()
      Rreturns LUT if defined.
      Returns:
      the LUT if defined else it is null

    • getSecondImage

      public int getSecondImage()
      Accessor that returns the address of the TIF header of the second image if present Returns zero if not present.
      Returns:
      secondImage

    • readImage

      public ModelImage readImage(boolean multiFile, boolean one) throws IOException
      Reads the Tiff header which indicates endianess, the TIFF magic number, and the offset in bytes of the first IFD. It then reads all the IFDs. This method then opens a Model of an image and imports the the images one slice at a time. Image slices are separated by an IFD.
      Parameters:
      multiFile - true if a set of files each containing a separate 2D image is present false if one file with either a 2D image or a stack of 2D images
      one - DOCUMENT ME!
      Returns:
      returns the image
      Throws:
      IOException - if there is an error reading the file

    • setFileName

      public void setFileName(String fName)
      Accessor to set the file name (used when reading TIFF multiFile).
      Parameters:
      fName - file name of image to read.

    • openIFD

      private boolean openIFD(FileInfoLSM fileInfo) throws IOException
      Reads and decodes IFDs (Image File Directory).
      Parameters:
      fileInfo - DOCUMENT ME!
      Returns:
      DOCUMENT ME!
      Throws:
      IOException - if there is an error reading the file

    • readBuffer

      private void readBuffer(int slice, float[] buffer) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - offset into the file stored in the dataOffset array
      buffer - buffer where the info is stored
      Throws:
      IOException - if there is an error reading the file

    • readCZPrivateTag

      private void readCZPrivateTag() throws IOException
      DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!

    • readDrawingElement

      private void readDrawingElement() throws IOException
      DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!

    • readKsData

      private void readKsData()
      DOCUMENT ME!

    • readLut

      private void readLut() throws IOException
      DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!

    • readOffsetAcquisitionParameters

      private void readOffsetAcquisitionParameters() throws IOException
      Throws:
      IOException

    • readOffsetChannelFactors

      private void readOffsetChannelFactors() throws IOException
      DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!

    • readOffsetCharacteristics

      private void readOffsetCharacteristics() throws IOException
      Throws:
      IOException

    • readOffsetPalette

      private void readOffsetPalette() throws IOException
      Throws:
      IOException

    • readOffsetPositions

      private void readOffsetPositions() throws IOException
      Throws:
      IOException

    • readOffsetTilePositions

      private void readOffsetTilePositions() throws IOException
      Throws:
      IOException

    • readOffsetUnmixParameters

      private void readOffsetUnmixParameters()
      DOCUMENT ME!

    • readScanInformation

      private void readScanInformation() throws IOException
      DOCUMENT ME!
      Throws:
      IOException - DOCUMENT ME!

    • readTileBuffer

      private void readTileBuffer(int slice, float[] buffer) throws IOException
      Reads a slice of data at a time and stores the results in the buffer.
      Parameters:
      slice - image slice
      buffer - buffer where the info is stored
      Throws:
      IOException - if there is an error reading the file