FW: MRXS question

Mon Sep 2 05:51:05 EDT 2024

Dear community,

I had asked this question in July, but no one replied. Does anyone know about this? If not, of course I will not ask again 😊

Thank you 

Martin

-----Original Message-----
From: Martin Weihrauch <m.weihrauch at smartinmedia.com> 
Sent: Dienstag, 30. Juli 2024 21:54
To: Martin Weihrauch <m.weihrauch at smartinmedia.com>; openslide-users at lists.andrew.cmu.edu
Subject: RE: MRXS question

There is another confusion I have about getting the size of largest zoom level in an mrxs slide.
Using the MRXS SDK from 3DHistech, I get WIDTH x HEIGHT
65,280 x 77,312

With ImageScope (Leica), I get for the same image:
76,032 x 78,080

From OpenSlide, I get:
53,587 x 75,273

I know about all this weird overlapping, etc. But how can I ultimately get (calculate?) the "real" resolution?

Below I paste all the information, which I could extract from the file (slideini.dat, etc).

Thanks

Martin
---

Group: GENERAL
================================
SLIDE_VERSION = 01.03
SLIDE_NAME = slide-2019-05-07T16-09-13-R1-S10 PROJECT_NAME = Pannoramic Slide Scanner SLIDE_ID = DB2FA4C030AA445EBCEB361FB15F63F1 IMAGENUMBER_X = 272 IMAGENUMBER_Y = 760 SLIDE_CREATION_FINISHED = True CURRENT_SLIDE_VERSION = 2.2 IMAGE_OVERLAP_MICROMETERS_X = 0 IMAGE_OVERLAP_MICROMETERS_Y = 0 SLIDE_POSITION_X = 3600 SLIDE_POSITION_Y = 22642 SLIDE_CONTENT = DIGITAL_SLIDE SLIDE_CREATIONDATETIME = 07/05/2019 16:09:36 VIMSLIDE_CAMERA_REAL_BITDEPTH = 24 CONFOCAL = NO DISK_POSITION = 0 FOCUS_MAP = AUTO FOCUS_LIMIT = DISABLED FLAT_FIELD_CORRECTION = DISABLED EXTENDED_FOCUS_ALGORITHM = FL Image VIMSLIDE_SLIDE_BITDEPTH = 8 CAMERA_TYPE = Point Grey GS3-U3-51S5M-C ADAPTER_SIZE = 0.63 OPTOVAR_SIZE = 1 OBJECTIVE_MAGNIFICATION = 20 OBJECTIVE_NAME = Plan-Apochromat SLIDE_TYPE = SLIDE_TYPE_BRIGHTFIELD CameraImageDivisionsPerSide = 8
Group: HIERARCHICAL
================================
INDEXFILE = Index.dat
PAGEELEMENTCOUNT = 128
PAGELENGTH = 2048
HIER_COUNT = 4
NONHIER_COUNT = 4
HIER_0_NAME = Slide zoom level
HIER_0_COUNT = 9
HIER_0_DEFAULT = 0
HIER_0_SECTION = LAYER_0_SECTION
HIER_0_VAL_0 = ZoomLevel_0
HIER_0_VAL_0_SECTION = LAYER_0_LEVEL_0_SECTION
HIER_0_VAL_1 = ZoomLevel_1
HIER_0_VAL_1_SECTION = LAYER_0_LEVEL_1_SECTION
HIER_0_VAL_2 = ZoomLevel_2
HIER_0_VAL_2_SECTION = LAYER_0_LEVEL_2_SECTION
HIER_0_VAL_3 = ZoomLevel_3
HIER_0_VAL_3_SECTION = LAYER_0_LEVEL_3_SECTION
HIER_0_VAL_4 = ZoomLevel_4
HIER_0_VAL_4_SECTION = LAYER_0_LEVEL_4_SECTION
HIER_0_VAL_5 = ZoomLevel_5
HIER_0_VAL_5_SECTION = LAYER_0_LEVEL_5_SECTION
HIER_0_VAL_6 = ZoomLevel_6
HIER_0_VAL_6_SECTION = LAYER_0_LEVEL_6_SECTION
HIER_0_VAL_7 = ZoomLevel_7
HIER_0_VAL_7_SECTION = LAYER_0_LEVEL_7_SECTION
HIER_0_VAL_8 = ZoomLevel_8
HIER_0_VAL_8_SECTION = LAYER_0_LEVEL_8_SECTION HIER_1_NAME = Slide filter level HIER_1_COUNT = 3 HIER_1_DEFAULT = 0 HIER_1_SECTION = LAYER_1_SECTION
HIER_1_VAL_0 = FilterLevel_0
HIER_1_VAL_0_SECTION = LAYER_1_LEVEL_0_SECTION
HIER_1_VAL_1 = FilterLevel_1
HIER_1_VAL_1_SECTION = LAYER_1_LEVEL_1_SECTION
HIER_1_VAL_2 = FilterLevel_2
HIER_1_VAL_2_SECTION = LAYER_1_LEVEL_2_SECTION HIER_2_NAME = Microscope focus level HIER_2_COUNT = 1 HIER_2_DEFAULT = 0 HIER_2_SECTION = LAYER_2_SECTION
HIER_2_VAL_0 = ExtFocusLevel
HIER_2_VAL_0_SECTION = LAYER_2_LEVEL_0_SECTION HIER_3_NAME = Scan info layer HIER_3_COUNT = 2 HIER_3_DEFAULT = 0 HIER_3_SECTION = LAYER_3_SECTION
HIER_3_VAL_0 = ScanInfoLayer_DefaultLevel HIER_3_VAL_0_SECTION = LAYER_3_LEVEL_0_SECTION
HIER_3_VAL_1 = ScanInfoLayer_XMLInfoLevel HIER_3_VAL_1_SECTION = LAYER_3_LEVEL_1_SECTION NONHIER_0_NAME = Scan data layer NONHIER_0_COUNT = 10 NONHIER_0_SECTION = NONHIERLAYER_0_SECTION
NONHIER_0_VAL_0 = ScanDataLayer_ScanMap
NONHIER_0_VAL_0_SECTION = NONHIERLAYER_0_LEVEL_0_SECTION NONHIER_0_VAL_0_IMAGENUMBER_X = 1 NONHIER_0_VAL_0_IMAGENUMBER_Y = 1
NONHIER_0_VAL_1 = ScanDataLayer_XMLInfoHeader NONHIER_0_VAL_1_SECTION = NONHIERLAYER_0_LEVEL_1_SECTION NONHIER_0_VAL_1_IMAGENUMBER_X = 1 NONHIER_0_VAL_1_IMAGENUMBER_Y = 1
NONHIER_0_VAL_2 = ScanDataLayer_SlideThumbnail NONHIER_0_VAL_2_SECTION = NONHIERLAYER_0_LEVEL_2_SECTION NONHIER_0_VAL_2_IMAGENUMBER_X = 1 NONHIER_0_VAL_2_IMAGENUMBER_Y = 1
NONHIER_0_VAL_3 = ScanDataLayer_SlideBarcode NONHIER_0_VAL_3_SECTION = NONHIERLAYER_0_LEVEL_3_SECTION NONHIER_0_VAL_3_IMAGENUMBER_X = 1 NONHIER_0_VAL_3_IMAGENUMBER_Y = 1
NONHIER_0_VAL_4 = ScanDataLayer_SlidePreview NONHIER_0_VAL_4_SECTION = NONHIERLAYER_0_LEVEL_4_SECTION NONHIER_0_VAL_4_IMAGENUMBER_X = 1 NONHIER_0_VAL_4_IMAGENUMBER_Y = 1
NONHIER_0_VAL_5 = ScanDataLayer_StagePositionMap NONHIER_0_VAL_5_SECTION = NONHIERLAYER_0_LEVEL_5_SECTION NONHIER_0_VAL_5_IMAGENUMBER_X = 1 NONHIER_0_VAL_5_IMAGENUMBER_Y = 1
NONHIER_0_VAL_6 = ScanDataLayer_Empty
NONHIER_0_VAL_6_SECTION = NONHIERLAYER_0_LEVEL_6_SECTION NONHIER_0_VAL_6_IMAGENUMBER_X = 1 NONHIER_0_VAL_6_IMAGENUMBER_Y = 1
NONHIER_0_VAL_7 = ProfileXMLHeader
NONHIER_0_VAL_7_SECTION = NONHIERLAYER_0_LEVEL_7_SECTION NONHIER_0_VAL_7_IMAGENUMBER_X = 1 NONHIER_0_VAL_7_IMAGENUMBER_Y = 1
NONHIER_0_VAL_8 = ProfileXML
NONHIER_0_VAL_8_SECTION = NONHIERLAYER_0_LEVEL_8_SECTION NONHIER_0_VAL_8_IMAGENUMBER_X = 1 NONHIER_0_VAL_8_IMAGENUMBER_Y = 1
NONHIER_0_VAL_9 = ScannedFOVsMap
NONHIER_0_VAL_9_SECTION = NONHIERLAYER_0_LEVEL_9_SECTION NONHIER_0_VAL_9_IMAGENUMBER_X = 1 NONHIER_0_VAL_9_IMAGENUMBER_Y = 1 NONHIER_1_NAME = StitchingLayer NONHIER_1_COUNT = 1 NONHIER_1_SECTION = NONHIERLAYER_1_SECTION
NONHIER_1_VAL_0 = DataLevel_V1.0
NONHIER_1_VAL_0_SECTION = NONHIERLAYER_1_LEVEL_0_SECTION NONHIER_1_VAL_0_IMAGENUMBER_X = 1 NONHIER_1_VAL_0_IMAGENUMBER_Y = 1 NONHIER_2_NAME = StitchingIntensityLayer NONHIER_2_COUNT = 1 NONHIER_2_SECTION = NONHIERLAYER_2_SECTION
NONHIER_2_VAL_0 = StitchingIntensityLevel NONHIER_2_VAL_0_SECTION = NONHIERLAYER_2_LEVEL_0_SECTION NONHIER_2_VAL_0_IMAGENUMBER_X = 2 NONHIER_2_VAL_0_IMAGENUMBER_Y = 1 NONHIER_3_NAME = VIMSLIDE_HISTOGRAM_DATA NONHIER_3_COUNT = 1 NONHIER_3_SECTION = NONHIERLAYER_3_SECTION
NONHIER_3_VAL_0 = default
NONHIER_3_VAL_0_SECTION = NONHIERLAYER_3_LEVEL_0_SECTION NONHIER_3_VAL_0_IMAGENUMBER_X = 1 NONHIER_3_VAL_0_IMAGENUMBER_Y = 1
Group: DATAFILE
================================
FILE_COUNT = 21
FILE_0 = Data0000.dat
FILE_1 = Data0001.dat
FILE_2 = Data0002.dat
FILE_3 = Data0003.dat
FILE_4 = Data0004.dat
FILE_5 = Data0005.dat
FILE_6 = Data0006.dat
FILE_7 = Data0007.dat
FILE_8 = Data0008.dat
FILE_9 = Data0009.dat
FILE_10 = Data0010.dat
FILE_11 = Data0011.dat
FILE_12 = Data0012.dat
FILE_13 = Data0013.dat
FILE_14 = Data0014.dat
FILE_15 = Data0015.dat
FILE_16 = Data0016.dat
FILE_17 = Data0017.dat
FILE_18 = Data0018.dat
FILE_19 = Data0019.dat
FILE_20 = Data0020.dat
Group: LAYER_0_LEVEL_0_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 0.275739701721575 MICROMETER_PER_PIXEL_Y = 0.275739701721575 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 110.223652173913 OVERLAP_Y = 110.223652173913 IMAGE_CONCAT_FACTOR = 0 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_1_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 0.55147940344315 MICROMETER_PER_PIXEL_Y = 0.55147940344315 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 55.1118260869565 OVERLAP_Y = 55.1118260869565 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_2_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 1.10249342342348 MICROMETER_PER_PIXEL_Y = 1.10239892931935 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 27.5559130434783 OVERLAP_Y = 27.5559130434783 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_3_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 2.20406733606845 MICROMETER_PER_PIXEL_Y = 2.20369435620695 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 13.7779565217391 OVERLAP_Y = 13.7779565217391 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_4_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 4.40630708728113 MICROMETER_PER_PIXEL_Y = 4.405198161364 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 6.88897826086957 OVERLAP_Y = 6.88897826086957 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_5_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 8.81261417456226 MICROMETER_PER_PIXEL_Y = 8.810396322728 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 3.44448913043478 OVERLAP_Y = 3.44448913043478 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_6_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 17.6179512110778 MICROMETER_PER_PIXEL_Y = 17.6120781090339 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 1.72224456521739 OVERLAP_Y = 1.72224456521739 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_7_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 35.2213661587802 MICROMETER_PER_PIXEL_Y = 35.2067529788296 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 0.861122282608696 OVERLAP_Y = 0.861122282608696 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_0_LEVEL_8_SECTION
================================
IMAGE_FILL_COLOR_BGR = 16777215
MICROMETER_PER_PIXEL_X = 70.4427323175603 MICROMETER_PER_PIXEL_Y = 70.4135059576593 DIGITIZER_WIDTH = 303 DIGITIZER_HEIGHT = 253 OVERLAP_X = 0.430561141304348 OVERLAP_Y = 0.430561141304348 IMAGE_CONCAT_FACTOR = 1 IMAGE_FORMAT = JPEG IMAGE_COMPRESSION_FACTOR = 80
Group: LAYER_1_LEVEL_0_SECTION
================================
ZSTACK_STEP_COUNT = 0
ZSTACK_FIRST_LEVEL = 0
FILTER_NAME =
ZDIFF = -1
XDIFF = 0
YDIFF = 0
COLOR_R = 0
COLOR_G = 0
COLOR_B = 0
USE_RED_CHANNEL = False
USE_GREEN_CHANNEL = False
USE_BLUE_CHANNEL = False
FILTER_REAL_POSITION = 0
IS_MASTER_FILTER = True
STORING_CHANNEL_NUMBER = 0
IS_STITCHING_FILTER = True
ACTIVE = ON
MODIFY = ON
THRESHOLD = 0
DATA_IN_THIS_FILTER_LEVEL = FilterLevel_0 EXPOSUREPERCENTAGE = 0 DIGITALGAIN = 0 EXTENDED_STEP_SIZE = 0 EXTENDED_STEP_COUNT = 1 VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE = 256 EXCITATION_WAVELENGTH = 0 EXCITATION_BANDWIDTH = 0 EMISSION_WAVELENGTH = 0 EMISSION_BANDWIDTH = 0
Group: LAYER_1_LEVEL_1_SECTION
================================
ZSTACK_STEP_COUNT = 0
ZSTACK_FIRST_LEVEL = 0
FILTER_NAME =
ZDIFF = -1
XDIFF = 0
YDIFF = 0
COLOR_R = 0
COLOR_G = 0
COLOR_B = 0
USE_RED_CHANNEL = False
USE_GREEN_CHANNEL = False
USE_BLUE_CHANNEL = False
FILTER_REAL_POSITION = 0
IS_MASTER_FILTER = False
STORING_CHANNEL_NUMBER = 1
IS_STITCHING_FILTER = False
ACTIVE = ON
MODIFY = ON
THRESHOLD = 0
DATA_IN_THIS_FILTER_LEVEL = FilterLevel_0 EXPOSUREPERCENTAGE = 0 DIGITALGAIN = 0 EXTENDED_STEP_SIZE = 0 EXTENDED_STEP_COUNT = 1 VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE = 256 EXCITATION_WAVELENGTH = 0 EXCITATION_BANDWIDTH = 0 EMISSION_WAVELENGTH = 0 EMISSION_BANDWIDTH = 0
Group: LAYER_1_LEVEL_2_SECTION
================================
ZSTACK_STEP_COUNT = 0
ZSTACK_FIRST_LEVEL = 0
FILTER_NAME =
ZDIFF = -1
XDIFF = 0
YDIFF = 0
COLOR_R = 0
COLOR_G = 0
COLOR_B = 0
USE_RED_CHANNEL = False
USE_GREEN_CHANNEL = False
USE_BLUE_CHANNEL = False
FILTER_REAL_POSITION = 0
IS_MASTER_FILTER = False
STORING_CHANNEL_NUMBER = 2
IS_STITCHING_FILTER = False
ACTIVE = ON
MODIFY = ON
THRESHOLD = 0
DATA_IN_THIS_FILTER_LEVEL = FilterLevel_0 EXPOSUREPERCENTAGE = 0 DIGITALGAIN = 0 EXTENDED_STEP_SIZE = 0 EXTENDED_STEP_COUNT = 1 VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE = 256 EXCITATION_WAVELENGTH = 0 EXCITATION_BANDWIDTH = 0 EMISSION_WAVELENGTH = 0 EMISSION_BANDWIDTH = 0
Group: LAYER_2_SECTION
================================
EXTENDED_FOCUS_LEVEL = -1
ZERO_FOCUS_LEVEL = 0
LAST_Z_STACKED_ZOOM_LEVEL = 9
Group: LAYER_2_LEVEL_0_SECTION
================================
OFFSET_IN_MICROMETERS = 0
Group: LAYER_0_SECTION
================================
SHARPENED = 16
Group: NONHIERLAYER_0_LEVEL_0_SECTION
================================
SCANMAP_IMAGE_TYPE = PNG
SCANMAP_IMAGE_WIDTH = 34
SCANMAP_IMAGE_HEIGHT = 95
Group: NONHIERLAYER_0_LEVEL_5_SECTION
================================
STAGEPOSMAP_IMAGE_TYPE = PNG
STAGEPOSMAP_IMAGE_WIDTH = 34
STAGEPOSMAP_IMAGE_HEIGHT = 95
Group: NONHIERLAYER_0_LEVEL_2_SECTION
================================
THUMBNAIL_IMAGE_TYPE = JPEG
THUMBNAIL_IMAGE_WIDTH = 1453
THUMBNAIL_IMAGE_HEIGHT = 3305
Group: NONHIERLAYER_0_LEVEL_3_SECTION
================================
BARCODE_IMAGE_TYPE = JPEG
BARCODE_IMAGE_WIDTH = 1776
BARCODE_IMAGE_HEIGHT = 1406
BARCODE_IMAGE_FLIP = True
Group: NONHIERLAYER_0_SECTION
================================
SCANNER_HARDWARE_VERSION = Pannoramic SCAN 150 SCANNER_SOFTWARE_VERSION = 2.0.5.93613 SCANNER_CAMERA_TYPE = Point Grey GS3-U3-51S5M-C SCANNER_HARDWARE_ID = SC150-214805 OBJECT_GUIDE_HYSTERESIS_X = 54 OBJECT_GUIDE_HYSTERESIS_Y = 54 AVEGARE_IMAGE_OVERLAP_X_IN_PIXELS = 110.223652173913 AVEGARE_IMAGE_OVERLAP_Y_IN_PIXELS = 110.223652173913 CAMERA_ROTATION = 0 IccProfileColorScheme = 0 IccProfileWhitePoint = 0 IccProfileGamma = 2 SCANNING_TIME_IN_SEC = 93 SCANNED_FOV_COUNT = 440
Group: NONHIERLAYER_1_SECTION
================================
DATA_FORMAT_VERSION = 258
Group: NONHIERLAYER_2_LEVEL_0_SECTION
================================
COMPRESSSED_STITCHING_VERSION = 1
COMPRESSSED_STITCHING_TABLE_WIDTH = 34
COMPRESSSED_STITCHING_TABLE_HEIGHT = 95
COMPRESSSED_STITCHING_ORIG_CAMERA_TILE_WIDTH = 2424 COMPRESSSED_STITCHING_ORIG_CAMERA_TILE_HEIGHT = 2024 COMPRESSED_STITCHING_ORIG_CAMERA_TILE_OVERLAP_X = 108 COMPRESSED_STITCHING_ORIG_CAMERA_TILE_OVERLAP_Y = 108 COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__LEFT = 11636 COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__TOP = 67344 COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__RIGHT = 65223 COMPRESSED_STITCHING_ORIG_SLIDE_SCANNED_AREA_IN_PIXELS__BOTTOM = 142617
Group: NONHIERLAYER_3_SECTION
================================
VIMSLIDE_HISTOGRAM_DATA_CHANNEL_NUM = 3
VIMSLIDE_HISTOGRAM_DATA_FORMAT_VERSION = 257 VIMSLIDE_HISTOGRAM_DATA_CHANNEL_SIZE = 256
Group: NONHIERLAYER_0_LEVEL_4_SECTION
================================
PREVIEW_IMAGE_TYPE = JPEG
PREVIEW_IMAGE_WIDTH = 616
PREVIEW_IMAGE_HEIGHT = 1422