Image-related record format

*The interpretation of the Advanced part is only available in EN.

Image processing record (IPR)

Image processing record (IPR) file is designed to record the whole-life information of a microscope image from photo-taking to processing. Each staining image (ssDNA/DAPI, IF, H&E) includes six basic groups, "ImageInfo", "QCInfo", "Stitch", "TissueSeg", "CellSeg", and "Register", which are used to store microscopy photo-taking information, image quality control information, image stitching records, tissue segmentation records, cell segmentation records (optional), and registration records.

ItemDescription
AttributeDescription
IPRVersionIPR file format version.
DatesetDescription
PreviewA 2D matrix merges stitched image, tissue segmentation boundary and cell segmentation boundary.
/<stainType>/ImageInfo: Group records basic image information.
AttributesDescription
AppFileVerMicroscope software version.
BackgroundBalanceBackground balance.
BitDepthThe bit-depth of a camera sensor describes its ability to transform the analog signal coming from the pixel array into a digital signal.
BrightnessRelative intensity affecting a person or sensor.
ChannelCountNumber of RGB channels.
ColorEnhancementWhether enhanced image color display or not.
ContrastThe difference in color and intensity of the depicted object from its background.
DeviceSNMicroscope device serial number.
DistortionCorrectionWhether fixed distortion or not.
ExposureTimeExposure time in ms.
FOVHeightHeight of an individual FOV in pixel.
FOVWidthWidth of an individual FOV in pixel.
GainAmplification applied to the signal by the image sensor.
GammaThe coefficient links between the human eye and the digital camera.
GammaShiftWhether adapt the digital image taken with the help of a linearly recording camera to the nonlinear perception of the human eye or not.
IlluminanceIntensity of light.
ManufacturerMicroscope manufacturer.
ModelMicroscope model.
OverlapOverlapping pixels between single tiles.
PixelSizeXSize of pixel in x direction.
PixelSizeYSize of pixel in y direction.
QCResultFilePrefix of ImageQC/ImageStudio result file, the unique identifier of the image.
ScanChannelFluorescence channel.
ScanColsNumber of columns scanned.
ScanObjectiveMagnification power of the scan objective lens.
ScanRowsNumber of rows scanned.
ScanTimeScan date and time.
SharpnessDegree of clarity of the edge(s) of the image.
STOmicsChipFovRowStereo-seq Chip mask‘s FOV row.
STOmicsChipFovColStereo-seq Chip mask‘s FOV column.
RegisterVersionImage auto-processing & matrix registration software version.
StitchedImageWhether the corresponding image is a panorama image (true) or a set of tiled images (false).
STOmicsChipSNStereo-seq Chip serial number.
WhiteBalanceAn adjustment in electronic and film imaging that corrects the color balance of the lighting.
DatasetDataType: 1D arrayDescription
RGBScaleRGB color.
/<stainType>/QCInfo: Group records the QC information of the image.
AttributesDescription
ExperimenterEmail of the experimenter who did QC for the image.
GoodFOVCountNumber of FOVs that have identified more than 3 track cross points.
ImageQCVersionImage QC version.
QCPassFlagWhether the corresponding image passed QC.
RemarkInfoAny remarks, notes, comments on the image.
StainTypeStain type of microscopy image.
TotalFOVCountTotal number of FOVs.
TrackLineScore
Reference score for evaluating whether the detected track lines can be used as references for image stitching and registering with gene expression matrix. (This score only evaluate whether the program detected track lines on the image, it does not infer the clarity of the lines or the images).
TrackLineChannelShooting channel of track lines.
TrackCrossQCPassFlagWhether the QC of the track-cross point is passed.
ScopeStitchQCScoreScore to assess the stability of microscope overlap (DAPI & mIF only).
ScopeStitchQCPassFlagWhether the QC of microscope stitch is passed (DAPI & mIF only).
TemplateValidAreaProportion of encircled area by the detected points that match the global track line template (within the error range of 5 pixels), to the entire image area.
TemplateRecallProportion of detected points, which match the global track line template (within the error range of 5 pixels), to the points derived from the chip track line rules.
DatasetDataType: 2D arrayDescription
ScopeStitchQCMatrixMatrix of overlap deviation of each microscope FOV (DAPI & mIF only).
CrossPoints/row_col*n
Group of datasets for each FOV that records the track cross point coordinates. (Row and col stand for the FOV row and column index number, and n stands for number of FOVs). Each dataset is a 2D array record, (x, y) coordinates of track cross points in each FOV.
/<stainType>/Calibration: Group records the calibration information (<protein>_IF only).
AttributesDescription
CalibrationQCPassFlagWhether the calibration QC of IF image is passed.
/<stainType>/Calibration/Scope:
AttributesDescription
ConfidenceCalibration confidence of microscope-stitched tiled image vs. IF.
OffsetXHorizontal offset.
OffsetYvertical offset.
[optional]/<stainType>/Calibration/Stereo:
AttributesDescription
ConfidenceCalibration confidence of Stereo-stitched image vs. IF.
OffsetXHorizontal offset.
OffsetYVertical offset.
/<stainType>/Stitch: Group records the stitching information.
AttributesDescription
StitchingScoreReference score for stitching.
TemplateSourceThe reference FOV for deriving the template used for rotating and scaling the microscopic images.
WhichStitchStitching method for image, including microscope, template and ripple stitching. The default for stitched image is microscope.
DatasetDataType: 2D arrayDescription
TemplatePoint
Center coordinates for deriving template lines.
TransformTemplateCoordinates of template points registered with expression matrix.
/<stainType>/Stitch/StereoStitch: Group records the image stitching information processed by Stereo program.
AttributesDescription
StitchedGlobalHeightHeight of stitched tiled images using Stereo stitching algorithm. Tiled image only.
StitchedGlobalWidthWidth of stitched tiled images using Stereo stitching algorithm. Tiled image only.
DatasetDataType: 2D arrayDescription
StitchedGlobalLocCoordinates for the Stereo stitched tiled image. Tiled image only.
/<stainType>/Stitch/ScopeStitch: Group records the image stitching information processed by microscope imaging software.
AttributesDescription
GlobalHeightHeight of panorama image.
GlobalWidthWidth of panorama image.
DatasetDataType: 2D arrayDescription
GlobalLocCoordinates for the stitched tiled image (either program stitched or microscope stitched).
ScopeJitterDiffJitter offset of microscope stitching.
ScopeHorizontalJitterHorizontal jitter offset of microscope stitching. Tiled image only.
ScopeVerticalJitterVertical jitter offset of microscope stitching. Tiled image only.
/<stainType>/Stitch/StitchEval: Group records the evaluation result of stitching.
AttributeDescription
MaxDeviationMaximum stitching deviation.
DatasetDataType: 2D arrayDescription
GlobalDeviationGlobal stitching deviation matrix. Tiled image only.
StitchEvalHStitching deviation matrix for the horizontal axes.
StitchEvalVStitching deviation matrix for the vertical axes.
/<stainType>/Register: Group records the information that aligns images with gene expression matrix.
AttributesDescription
CounterRot90Count of counter-clockwise rotation of 90 degrees.
FlipWhether horizontally flipped or not.
MatrixShapeHeight and width of the gene expression matrix.
OffsetXOffset between microscope image and gene expression matrix in x-axis.
OffsetYOffset between microscope image and gene expression matrix in y-axis.
RegisterScoreReference score for registration.
RotationRotation degree between raw image and deviation template.
ScaleXScale between raw image and deviation template in horizontal direction.
ScaleYScale between raw image and deviation template in vertical direction.
XStartGene expression matrix offset x (GEF geneExp/binN/expression attribute minX).
YStartGene expression matrix offset y (GEF geneExp/binN/expression attribute minY).
ManualRotationManual rotation degree of the raw image around the center point.
ManualScaleXManual scale of the raw image in horizontal direction based on center point.
ManualScaleYManual scale of the raw image in vertical direction based on center point.
DatasetDataType: 2D arrayDescription
MatrixTemplateList of track cross points derived from gene expression matrix.
/<stainType>/TissueSeg: Group records the tissue segmentation information.
AttributesDescription
TissueSegScoreReference score for tissue segmentation.
TissueSegShapeImage shape for tissue segmentation mask image.
ThresholdThe threshold for tissue segmentation in IF images is divided into maximum and minimum values (IF only).
DatasetDataType: 2D arrayDescription
TissueMaskEncoded tissue segmentation mask file (after registration with gene expression matrix).
/<stainType>/CellSeg: Group records the cell segmentation information.
AttributesDescription
CellSegShapeImage shape for cell segmentation mask image.
DatasetDataType: 2D arrayDescription
CellMaskEncoded cell segmentation mask file (after registration with gene expression matrix).
CellSegTraceCell contour attributes, including height, width and area.
/StereoResepSwitch: Group stores the state of each module that whether the module needs to be performed.
AttributesDescription
stitchSwitch for performing stitching.
tissuesegSwitch for performing tissue segmentation.
cellsegSwitch for performing cell segmentation.
registerSwitch for performing registration.
/ManualState: Group stores the state of each module that whether the module has been manually processed.
AttributesDescription
stitchWhether manually stitched the tiled images.
tissuesegWhether manually delineated the tissue coverage region.
cellsegWhether manually delineated the cell coverage regions.
registerWhether manually aligned microscope image and gene expression matrix.
calibrationWhether manually calibrated two images. For example, manually match IF image with DAPI image.

Recorded image processing (RPI)

The image pyramid model is a multi-resolution hierarchical model that is used to store and display images in different resolutions. For the same field of view, the layer of the image pyramid that is closest to the bottom includes the most detailed information and has the largest scale. register pipeline performs the down-sampling step on the registered image, and the result images are layered to construct a pyramid with the suffix ".rpi". For each resolution layer, the intact registered image is split into 256 pixels x 256 pixels tiles. If the size of a layer is smaller than 256 x 256, the image will then remain intact. The outer layer group of RPI file is defined according to its stain type, generally including ssDNA, DAPI, IF (immunofluorescence image especially for protein, group name as <protein_IF>), and H&E. In each group of stain types, multiple image results, including an image subgroup (registered microscopy image), a TissueMask subgroup (registered mask boundary for the tissue coverage area), and a CellMask subgroup (registered mask boundaries for the cell coverage area, optional), could be saved respectively.

Schematic diagram of the image pyramid:

Image pyramid displaying

Item Description
Attributes Description
imgSize Size of the image.
sizex Max of x.
sizey Max of y.
version RPI file version.
x_start Offset x of the matrix.
y_start Offset y of the matrix.
/\/\: Group records the specific layer information, mainly including "Image", "TissueMask", "CellMask" and "CellMask_adjusted".
Attributes Description
MaxGrayLevel Maximum gray value.
MinGrayLevel Minimum gray value.
GrayLevelElbow Elbow point of gray value.
TrackLayer Whether track layer.
Color Layer color.
Groups Description
binN Detailled downsampling metadata for each bin size.
© 2025 STOmics Tech. All rights reserved.Modified: 2025-03-07 10:28:04

results matching ""

    No results matching ""