SciServer at MedHacks 2021
IDIES is providing a subset of the data underlying work in the AstroPathTM Collaboration to participants in MedHacks2021; those data are provided in a Data Volume called AstroPath Data Public. To access them through SciServer, create any new compute image and select the Data Volume to mount it.
The AstroPath Public Data Volume contains a notebook (working_with_AstroPath_data_using_SciServer.ipynb) with several examples of how the raw data can be used to kickstart analyses. That notebook will be presented interactively at the workshop on Saturday.
The raw data provided include:
- 1,801 multispectral immunofluorescence microscopy images in component .tif format for a single example slide
- A SQL database containing information about the images, their locations within the slide, and the cells they depict
Participants can use the test CellView site to conveniently browse whole-slide images, along with their annotations and identified cells. The slide whose images and database information are available is listed under Project01, slide M51_1.
Strong parallels between multispectral analyses in astronomy and emerging multiplexing platforms for pathology.
The next generation of tissue-based biomarkers are likely to be identified by use of large, well-curated datasets. To that end, image analysis approaches originally developed for astronomy were applied to pathology specimens to produce trillions of pixels of robust tissue imaging data and facilitate assay and atlas development.