napari based application

[pskeshu]

the user should be able to

• click snap button
• view image from the microscope
• view objects in the image
• view object information (xy coordinate of the object)

we would have to figure out

• how can we create a (using magicgui) snap button that calls a snap() in the backend and waits for the image to arrive from the hard-link, which is displayed as layers [image, segmented_object] in napari

references

start here: https://napari.org/tutorials/
and here: https://github.com/napari/magicgui

maybe as a plugin?: https://napari.org/docs/dev/plugins/for_plugin_developers.html

example application which is built on top of napari: https://github.com/quantumjot/BayesianTracker#Usage-with-Napari

[pskeshu]

once a bluesky run is over, one can access the data from the last run of the RE using header = db[-1].

more information at https://nsls-ii.github.io/databroker/v1/tutorial.html

[pskeshu]

https://nsls-ii.github.io/databroker/v2/user/index.html has some interesting concepts like discoverable catalogues

[pskeshu]

current simplified architecture

[pskeshu]

can we do 3d imaging + segmentation of DAPI HeLa?

[pskeshu]

how to do transformation between image coordinates and stage coordinates, which are physical entities?