For each experiment in your study:

• A list of Sample IDs associated with that experiment
• Ensure your images match one of the supported image types below

For your Metadata:

• Sample Traits: A csv table associating Sample IDs to Clinical Metadata. See the page on the sample traits table for more details on the formatting requirements for this csv.

Image format types:

For an overview of supported imaging assay types please see the Supported Assay Types reference page.

PhenoCycler Images

• PhenoCycler images require stitched, multi-channel TIF image stacks

  • Files should be TIF or QPTIFF (.tif, .ome.tif, or .qptif file extension)

  • The images should be stitched, not individual image tiles

  • Images can be represented in 2 ways:

    • 4 dimensions: Timestep, Channel, Y value, X value (TCXY), where each channel is a grayscale image
      • This stands in contrast with an RGB image which has the dimensions of 3 Channels, Y value, X value (CYX)
      • The different channels should be stacked in one file, with 4 channels per cycle, rather than uploading each channel individually
    • 3 dimensions: Channel, Y value, X value (CXY), where each channel is a grayscale image
      • This stands in contrast with an RGB image which are CYX images, with only 3 channels
      • Images should be stacked into a multi-channel image, rather than uploading each channel individually

    

    Example of a CODEX image with TCYX Dimensions. When opened in image software such as Fiji two sliders appear at the bottom of the image. The top one represents cycles, the bottom is channels.

IMC, MIBI, PhenoImager HT/Vectra Polaris, General Fluorescence Microscopy

• Files should be .tif, .ome.tif, or .qptif file extension

• Images should be stitched

• Images are represented with by 3 dimensions: Channel, Y value, X value (CXY), where each channel is a grayscale image

  • This stands in contrast with an RGB image which are CYX images, with only 3 channels

• Images should be stacked into a multi-channel image

  • i.e. If your biomarker panel has 40 biomarkers you should have a 40 channel image

• Please do not include images that have any type of additional dimensions like timestamps, additional focal planes (z stack), or cycles

  

  Example of a CYX image. Notice that when opened in Fiji, there is only a single slider at the bottom of the image, for exploring different image channels.

H&E, Immunohistochemistry (IHC), and other traditional brightfield imagery

• Files should be .tif, .ome.tif, .qptif, or .svs file extension
• Images should utilize the RGB color space