Harvard Tissue Atlas Harvard Medical School
Data

Multiplexed 3D analysis of cell plasticity and immune niches in melanoma

Yapp C, Nirmal AJ, Zhou F, Maliga Z, Llopis PM, Murphy GF, Lian CG, Danuser G, Santagata S, Sorger PK

bioRxiv Access Primary Data Contact


Curated Minerva Stories

Curated stories provide access to images that have undergone a quality control step to remove failed markers, ensure appropriate channel intensity settings, and provide metadata about the underlying sample and image. Click the Minerva story icon for an interactive view of the full-resolution images.

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Melanoma in-situ with 3D imaging
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Glioblastoma (GBM)- 3D CyCIF - LSP17378
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Lung metastasis (lungMET) - 3D CyCIF - LSP22408
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Metastatic melanoma - 3D CyCIF - LSP22409
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Melanoma VGP - 3D CyCIF - LSP13626
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Melanoma MIS - 3D CyCIF - LSP13625
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Melanoma VGP - 3D CyCIF - LSP13625
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STIC-TR3 - 3D CyCIF - LSP18251
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STIC-TR4 - 3D CyCIF - LSP18251
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STIC-TR5 - 3D CyCIF - LSP18251
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Tonsil - 3D CyCIF - LSP13357

Data Access

Access the full 3D Melanoma dataset

All images at full resolution are stored and can be accessed through Amazon Web Services (AWS) S3. AWS S3 bucket locations:

s3://lsp-public-data/yapp-2023-3d-melanoma/Dataset1-LSP13626-invasive-margin.ims

s3://lsp-public-data/yapp-2023-3d-melanoma/Dataset1-LSP13626-melanoma-in-situ.ims

To browse and download the data use either a graphical file transfer application that supports S3 such as CyberDuck, or the AWS CLI tools. A graphical tool may be more convenient but the CLI tools will likely offer higher download speeds.

Cyberduck or Graphical File Transfer Instructions:

Make sure anonymous login is selected, either through using the following server information: s3://anonymous@yapp-2023-3d-melanoma.s3.amazonaws.com/ or make sure the anonymous login button is selected.

AWS CLI Tips:

For users who wish to perform processing within AWS, note that the bucket is located in the us-east-1 region so any other resources must be instantiated in this same region.

Review your IAM permissions and add additional in-line policies, as needed. For example, use: aws s3 ls –no-sign-request s3://yapp-2023-3d-melanoma/data/. If you continue to experience issues using the CLI, please follow the instructions for using a GUI above or refer to AWS existing documentation.


Tips for viewing Images with Imaris

Here are some tips for getting started viewing .ims files using Imaris Viewer:

  1. To view the .ims images, download the free Imaris Viewer at: https://imaris.oxinst.com/imaris-viewer. View the recommended system requirements here.

  2. Open Imaris Viewer and, in the top left corner, select Surpass. Click and drag .ims file into Imaris Viewer.

  3. To view the channel/antibody list, select Edit > Image Properties.
    • Each channels’ brightness, contrast, and color can be adjusted here.
    • Tick the box to show or hide a channel. 8 channels is the maximum number of simultaneously viewable channels.
  4. Image navigation:
    • To zoom in and out -> use the mouse wheel
    • To orbit around -> use the left mouse button
    • To pan around -> use the right mouse button
  5. To switch to single plane viewing, select Slice in the top menu. Click on 3D View to return to 3D navigation mode.


Contact

Email tissue-atlas(at)hms.harvard.edu with the subject line “yapp-2023-3d-melanoma: Data Access” if you experience issues accessing the above S3 buckets. Please include the steps you have already tried to help us troubleshoot.