Virtual Microscope Improvements

openUC2 / ImSwitch

ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.

https://imswitch.readthedocs.io/

GNU General Public License v3.0

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Virtual Microscope Improvements #72

Open beniroquai opened 5 months ago

beniroquai commented 5 months ago

Some more ideas how we can contribute to smart microscopy by enhancing the Virtual Microscope Manager

Modalities

Light-sheet
general 3D stuff

More ideas

Different Noise models
Drift of the stage
Objective Switching
Different Samples
Bleaching
Multiple Channels / Laser behaviours
exposure time
add slm
load images from Remote / ZARR / Server, etc
OpenSlide / ZARR

Interfaces

REST API
Seperated PyPi package
Dockercontainer -> test it in different environments

CC: @hinderling @HannahSHeil @brunomsaraiva @jhnnsrs @henrypinkard @nornil @jacopoabramo

beniroquai commented 2 months ago

@hannahsheil, do you have a stitched stack of a multicolour high-resolution fluorescence sample somewhere by any chance for testing the multi-channel stuff? :)

beniroquai commented 2 months ago

@hinderling, how would you like to control the SLM in your opinion? Creating a REST Endpoint and upload patterns from a remote software? We do that with our SIM setup + raspi. Works !

HannahSHeil commented 2 months ago

@beniroquai , I had a very old (2021) 3-color sample. Are you aware of the file size of a 3 channel, stitched, z-stack? I'll send you the data and you might have to downsample ;) I just realized now, did you want a time stack?

beniroquai commented 2 months ago

Great idea with the time-axis ... but let's start with 4d first ^^