Dataverse Uploads

Contact Information

• Principal Investigator: Peter Sorger, Laboratory of Systems Pharmacology, Harvard Medical School ([email protected])
• Data Manager: Sarah Arena, Laboratory of Systems Pharmacology, Harvard Medical School ([email protected])

Harvard Dataverse Directory Structure

This repository references stories uploaded to the Harvard Dataverse. The many separate JPEG/PNG files in each Minerva Story have been compressed into additonal ZIP archives for easier management within the Dataverse. Each complete story referenced in this repository can be extracted from the dataverse as follows:

1. First, expand the dataverse_files.zip archive.
2. Then, move or copy STORY-NAME.zip to STORY-NAME.
3. Finally, expand the STORY-NAME.zip archive.

The unextracted directories will appear as follows:

├── README.md
'── STORY-NAME
  ├── STORY-NAME
  |   ├──- channel-group
  |   |   '── image tiles (.jpg)
  |   ├──- masks (optional)
  |   |   '── mask-group
  |   |      '── mask tiles (.png)
  |   '──- visdata (optional)
  |       '── visualizations (.csv)
  |── index.html
  '── img (optional)
      '── illustrations (.png)

Archive Extraction

To unpack the JPEG/PNG files into the proper location for correct functioning of the story, download and unzip the following zip archives into the corresponding directories:

• Unzip lin-2021-viz-97.zip within lin-2021-viz-97
• Unzip lin-2021-reg_96_97.zip within lin-2021-reg_96_97
• Unzip gaglia-2020-0813.zip within gaglia-2020-0813
• Unzip gaglia-2020-gemm-lung.zip within gaglia-2020-gemm-lung

The zip archive will be created a subdirectory with the same name as the parent, ie:

• lin-2021-viz-97/lin-2021-viz-97
• lin-2021-reg_96_97/lin-2021-reg_96_97
• gaglia-2020-0813/gaglia-2020-0813
• gaglia-2020-gemm-lung/gaglia-2020-gemm-lung

File Descriptions

• .zip: .zip archive containing JPEG/PNG pyramid files for multiple zoom levels to be assembled by a Minerva Story.
  • The JPEG files are rendered from fluorescence ome.tif images.
  • Optionally, PNG files are rendered segmentation masks from ome.tif images.
  • Optionally, CSV files are rendered to chart visualizations associated with the data.
• index.html: An html file generated from markdown files to publish the story online.
  • The HTML contains a JSON configuration output to control channel groups and waypoints.

File Naming Structure

• JPEG: channel-group/tile-location.jpg (e.g., AKT_34__AKT/0_0_7.jpg)
• PNG: mask-group/tile-location.png (e.g., TNP097_21types/0_0_7.png)