Transcript File

Pancreas_tx_file.csv : 5.2 GB
fov cell_ID cell x_local_px y_local_px x_global_px y_global_px z target CellComp
51 675 c_1_51_675 783 1005 53222.04 40920.41 4 CPA1 Nuclear
51 675 c_1_51_675 785 1005 53224.04 40920.41 5 CELA3B Nuclear
51 675 c_1_51_675 786 1005 53225.04 40920.41 4 SPINK1 Nuclear
51 675 c_1_51_675 786 1005 53225.04 40920.41 6 CELA3B Nuclear
51 675 c_1_51_675 787 1043 53226.04 40882.41 5 CELA3B Cytoplasm
51 675 c_1_51_675 787 1043 53226.04 40882.41 6 CELA3B Cytoplasm
51 675 c_1_51_675 787 1046 53226.04 40879.41 1 CELA3B Cytoplasm
51 675 c_1_51_675 784 1047 53223.04 40878.41 6 AKR7A2 Cytoplasm
51 680 c_1_51_680 1672 1075 54111.04 40850.41 7 P4HA2 Membrane
51 680 c_1_51_680 1665 1076 54104.04 40849.41 5 UAP1 Membrane





Cell Expression File

Pancreas_exprMat_file.csv : 2.1 GB
fov cell_ID A1BG ANXA5 ARF1 CPAMD8 CPB1 RPS5 RPS6 ZZZ3 Negative1 Negative2 SystemControl1 SystemControl2 …
51 999 0 0 0 16 6 0 0 0 0 0 0 0 …
51 1000 0 0 0 2 7 0 2 0 0 0 0 0 …
51 1001 0 0 2 5 1 0 0 0 0 0 0 0 …
51 1002 0 0 1 16 14 1 2 0 0 0 0 0 …
51 1003 0 2 2 32 31 4 4 0 0 0 0 0 …
51 1004 0 0 0 17 31 2 0 0 0 0 0 0 …
51 1005 0 0 6 26 22 0 8 0 0 0 0 0 …
51 1006 0 0 2 20 50 0 2 0 0 0 0 0 …
51 1007 0 0 2 13 7 0 2 0 0 0 0 0 …
51 1008 0 0 0 12 3 0 0 0 0 0 0 0 …





Cell Metadata File

Pancreas_metadata_file.csv : 11.4 MB
fov Area AspectRatio CenterX_local_px CenterY_local_px Width Height Mean.PanCK Max.PanCK Mean.CD68_CK8_18 Max.CD68_CK8_18 Mean.CD298_B2M Max.CD298_B2M Mean.CD45 Max.CD45 Mean.DAPI Max.DAPI cell_id X version Run_name Run_Tissue_name tissue Panel assay_type slide_ID CenterX_global_px CenterY_global_px cell_ID unassignedTranscripts nCount_RNA nFeature_RNA nCount_negprobes nFeature_negprobes nCount_falsecode nFeature_falsecode Area.um2 cell
51 5997 1.39 141 36 103 74 1565 5576 1701 6376 2799 8980 221 996 1155 3476 c_1_51_1 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 52580.04 41889.41 1 0.0781346 315 202 0 0 4 4 86.76163 c_1_51_1
51 1976 2.47 272 17 89 36 594 2260 154 636 930 1864 108 360 1126 2652 c_1_51_2 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 52711.04 41908.41 2 0.0781346 346 143 0 0 3 2 28.58779 c_1_51_2
51 2664 1.34 363 26 71 53 989 2812 135 728 1134 2400 92 320 794 1884 c_1_51_3 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 52802.04 41899.41 3 0.0781346 508 184 0 0 5 5 38.54144 c_1_51_3
51 8611 1.42 469 45 129 91 10538 43016 141 1068 4504 13796 115 896 1039 3324 c_1_51_4 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 52908.04 41880.41 4 0.0781346 1250 607 1 1 11 9 124.57969 c_1_51_4
51 5409 1.01 572 40 83 82 1452 9876 107 720 1327 11060 90 708 1988 3800 c_1_51_5 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 53011.04 41885.41 5 0.0781346 483 172 0 0 10 9 78.25474 c_1_51_5
51 4116 2.68 726 21 118 44 4687 23108 285 18592 4824 15556 212 11168 1906 3228 c_1_51_6 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 53165.04 41904.41 6 0.0781346 629 316 0 0 5 5 59.54825 c_1_51_6
51 5768 1.26 822 38 97 77 570 6304 106 2940 1418 20916 74 2864 1666 3576 c_1_51_7 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 53261.04 41887.41 7 0.0781346 878 332 0 0 14 10 83.44857 c_1_51_7
51 2859 1.98 1908 25 103 52 11695 36072 212 540 14515 50412 134 536 2029 3196 c_1_51_8 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 54347.04 41900.41 8 0.0781346 595 330 0 0 10 9 41.36260 c_1_51_8
51 3831 1.65 2171 27 91 55 435 1224 456 1588 2740 7148 51 420 965 4256 c_1_51_9 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 54610.04 41898.41 9 0.0781346 172 115 2 2 1 1 55.42501 c_1_51_9
51 5162 1.71 2303 28 99 58 144 1512 90 1480 342 2592 53 464 2100 5264 c_1_51_10 1 v6 Slide_S1 Pancreas Pancreas WTX RNA 1 54742.04 41897.41 10 0.0781346 309 157 0 0 1 1 74.68126 c_1_51_10




FOV Positions File

This file is used to reference each FOV within the global structure of the sample.
Pancreas_fov_positions_file.csv : 1.3 kB
Slide X_mm Y_mm Z_mm ZOffset_mm ROI FOV Order Run_Tissue_name
1 6.307417 5.042828 -0.034417 -2 0 51 67 Pancreas
1 6.307417 4.530908 -0.034663 -2 0 52 66 Pancreas
1 6.307417 4.018988 -0.034878 -2 0 53 65 Pancreas
1 6.819338 4.018988 -0.034577 -2 0 54 64 Pancreas
1 6.819338 4.530908 -0.034365 -2 0 55 63 Pancreas
1 6.819338 5.042828 -0.034124 -2 0 56 62 Pancreas
1 7.331259 5.042828 -0.033824 -2 0 57 61 Pancreas
1 7.331259 4.530908 -0.034063 -2 0 58 60 Pancreas
1 7.331259 4.018988 -0.034271 -2 0 59 59 Pancreas
1 6.190926 1.023840 -0.035615 -2 0 60 50 Pancreas


  • Column descriptions:
    • FOV
      • The Field Of View (FOV) number.
    • X_mm
      • The relative x position of the FOV, measured in millimeters.
    • Y_mm
      • See “X_mm” description, but in for the y dimension.
    • Z_mm
      • The relative z position of the FOV, measured in millimeters.
    • ZOffset_mm
      • Z offset in millimeters.
    • Order
      • Order in which the FOVs were collected.
    • Run_Tissue_name
      • Name of the slide
    • Slide
      • Slide number
    • ROI
      • Region of Interest
In latest version of AtoMx exported files, FOV postion file may also contain coordinates in px units.



Cell Polygons File

This file is a simple polygon descripton of cell boundries. These are provided as a graphical convenience but are only approximations of the cell boundries, which are fully defined by the cellLabels mask images.
Pancreas-polygons.csv : 66.3 MB
fov cellID cell x_local_px y_local_px x_global_px y_global_px
51 1 c_1_51_1 190 0 52629.04 41925.41
51 1 c_1_51_1 191 1 52630.04 41924.41
51 1 c_1_51_1 192 6 52631.04 41919.41
51 1 c_1_51_1 192 9 52631.04 41916.41
51 1 c_1_51_1 178 66 52617.04 41859.41
51 1 c_1_51_1 177 67 52616.04 41858.41
51 1 c_1_51_1 152 73 52591.04 41852.41
51 1 c_1_51_1 147 73 52586.04 41852.41
51 1 c_1_51_1 108 56 52547.04 41869.41
51 1 c_1_51_1 106 55 52545.04 41870.41


  • Column descriptions:
    • fov
      • The Field Of View (FOV) number.
    • cell_ID
      • Unique identifier for a single cell within a given FOV.
    • cell
      • Unique identifier for a single cell within the whole sample. Format ‘c_SLIDENUMBER_FOVNUMBER_CELLID’.
    • x_local_px
      • The x position of this transcript within the FOV, measured in pixels. To convert to microns multiply the pixel value by 0.12028 um per pixel.
    • y_local_px
      • Same as “x_local_px” but for the y dimension
    • x_global_px
      • The relative x position of the FOV, measured in pixels. To convert to microns multiply the pixel value by 0.12028 um per pixel. All FOVs are the same dimension, 4256 x 4256 pixels.
    • y_global_px
      • See “x_global_px” description, but in for the y dimension.



CellComposite Images

Each FOV has a CellComposite image that displays the ImmunoFluorescence intesity from the IHC markers selected for the SMI experiment.
CellComposite images are not included in AtoMx v1.3 software.

  • Channels
    • Green
      • PanCK
    • Red
      • CD45/GFAP
    • Yellow
      • CD68/CK8_18
    • Blue
      • DAPI



CellOverlay Images

Each FOV has a CellOverlay image that displays the cell boundries determined during cell segmentation, shown as cyan lines.



CellLabels Images

Each FOV has a CellLabels image that displays the cell definitions determined during cell segmentation. Each cell identified is given a unique number (cell_ID) and all pixels determined to be within that cell have an intensity value matching that number. These cell_ID values are shared in the transcript, Cell Expression, and Cell Metadata files. A pixel not assigned to a cell has a “0” value. To view this image we recommend opening in ImageJ or similar software that allows for brighness/contrast adjustments.



CompartmentLabels Images

Each FOV has a CompartmentLabels image that displays the subcellular compartment definitions determined during cell segmentation. Each compartment type is given a unique number and all pixels determined to be within that compartment type have an intensity value matching that number. To view this image we recommend opening in ImageJ or similar software that allows for brighness/contrast adjustments.

  • Compartment types
    1. Extracellular
    2. Nuclear
    3. Membrane
    4. Cytoplasmic



Seurat object

A preloaded Seurat object is also supplied. This object is compatible with the latest Seruat version (V5).
# Seurat ---------------------------------------------------------------------------
# packageVersion("Seurat")
# [1] ‘5.0.1’
library(Seurat)
library(SeuratObject)
panc <- readRDS("~/../Downloads/Seurat_Pancreas_withTranscripts.rds")

# check common plot types
Seurat::ImageDimPlot(object = panc, boundaries = "segmentation", molecules = c("COL1A1", "INS", "GCG"))
Pancreas WTx

Pancreas WTx 

# add cell typing results from InSituType
meta <- readRDS("~/../Downloads/Pancreas_celltype_InSituType.rds")
panc@meta.data$types <- meta[rownames(panc@meta.data), "cell_types"]
panc@meta.data$types[is.na(panc@meta.data$types)] <- "QC_dropped"

# zoom to single FOV
fox <- apply(panc@images$Pancreas$centroids@coords[panc@meta.data$fov %in% 52, ], 2, range)
options(future.globals.maxSize = 8000 * 1024^2)
zoom.crop <- Crop(panc[["Pancreas"]], x = fox[,"y"], y = fox[,"x"])
panc[["zoom1"]] <- zoom.crop
DefaultBoundary(panc[["zoom1"]]) <- "segmentation"
Seurat::ImageDimPlot(object = panc, fov = "zoom1", molecules = c("COL1A1", "INS", "GCG"), group.by = "types", mols.size = 1.5)
Pancreas WTx, single FOV

Pancreas WTx, single FOV