Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Improve speed of immunoProfile read #1

jim-bo opened this issue Nov 20, 2019 · 1 comment


Copy link

@jim-bo jim-bo commented Nov 20, 2019

Would it be possible to update the read_InFormImmunoProfileV1 function to avoid calculating NN, edge and contact maps to improve the loading time?


This comment has been minimized.

Copy link

@jason-weirather jason-weirather commented Nov 20, 2019

The most recent update 848b4eb
adds two additional parameters that can speed up an immuno-profile data read. There was already one parameter present which could be helpful to speed up a read.

From the updated documentation read_InFormImmunoProfileV1:

skip_margin (bool) – if false (default) read in margin line and define a margin according to steps. if true, only read a tumor and stroma.

skip_segmentation_processing – if false (default), it will store the cellmap and edgemap images, if true, it will skip these steps to save time but downstream applications will not be able to generate the cell-cell contact measurements or segmentation images.

skip_all_regions (bool) – if false (default), it will use drawn tumor masks or drawn tumor masks with drawn margins to calculate region areas, and assign cells to regions. If true it will assign all cells the default region of ‘Any’ and use the processed image.

These options will result in the loss of some data being available for downstream analysis so apply them with care.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
None yet
2 participants
You can’t perform that action at this time.