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.

Sign up for GitHub

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

Jump to bottom

Make Poster #3

Open

todd-fallesen opened this issue May 13, 2024 · 1 comment

Assignees

Collaborator

todd-fallesen commented May 13, 2024

Make Poster for ELMI 2024

todd-fallesen assigned todd-fallesen and vanessadao31

Collaborator Author

todd-fallesen commented May 13, 2024

- Outline:

Image Acquisition and Motivation

A little bit about the light sheet microscopy. A real image from the light sheet
Showing that the sizes of the structures are very different in size
Saying that they are all important

Segmentation pipeline using CellPose and Trackmate.

The FIJI script that does trackmate automatically on many pixel sizes
How we run the segmentations overnight, and then save the XML file to load and do some cleanup
Explain why we're doing the human in the loop segmentation, as opposed to straight up 3D cellposse

Combining the Segmentations

Explain why again we have multiple segmentations
Show the Napari plugin so that people can visualize the overlaps
Show that we can allow a range of 0 overlap allowed to a lot of overlap

Show how well it works

Show the results of some metrics on the trained data vs what we got from the pipeline
Show a final product from the napari plugin
link to the git with a QR code

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment