Hi Fans of Feedback Microscopy,

what would you do when you have access to the pixel stream from @zeiss-microscopy.bsky.social inside @napari.org?

Btw, it works as well in Fiji&ImageJ :-)

Sidenote: Experiments started from "outside" do not update the ZEN UI. But they are executed by ZENservice.

You need to add our ZEN API interface to that site?

github.com/zeiss-micros...

Guess what i am just doing ...?

Hi Fans of Smart Microscopy,

Are you ready to automate your next large scale microscopy experiment and work smarter, not harder?

Join us for the Smart Microscopy workshop organized by EPFL Bio-Imaging Platform (Lausanne) and @zeiss-microscopy.bsky.social

www.zeiss.ch/mikroskopie/...

I saw this in my vaccation in a cafe in France.
As a person creating AI software tools I hope that is not true but I am not so sure anymore ...

I finally managed to upload the first version of the napari-czitools plugin (still in alpha - expect issues...)

- open complete CZI images or subsets
- read CZI metadata

pypi.org/project/napa...

or

github.com/sebi06/napar...

The 1st working version of my little @napari.org plugin (napari-czitools) is almost ready.

It contains sample data, allows to read CZI metadata and can read CZI images (or parts of it) by using the sliders to crop what should be read.

Still quite some things to improve ...

Live from the @ai4life.bsky.social community meeting - the new ZEN Microscopy Copilot from @zeiss-microscopy.bsky.social "knows" about BioImageIO :-)

We now published the 1st version of our ZEN API examples from @zeiss-microscopy.bsky.social on our Github page:

github.com/zeiss-micros...

Control ZEN system from the outside using python (or any other language). Or stream the incoming pixel directly into a an array of online processing :-)

Looking forward to the AI4Life community event in Helsinki.

ai4life.eurobioimaging.eu/event/ai4lif...

For all fans of smart, data-driven microscopy:

- Guided Acquisition running on a Celldiscoverer 7
- overnight experiment (fully automated)
- mitotic events detected in overview image (over time)
- 300 3D stacks were acquired using high-resolution water immersion

If one wants to push the limits even further ZEN also offers to use the "PixelStream" directly in your client software using the ZEN API.

The stream of pixel will be directly availabe as an array, which one can use directly. Here an example for using a simple DL model for online segmentation.

And here is what can be achieved by using Guided Acquistion running on a Celldiscoverer 7 in just one overnight experiment in a fully automated fashion:

- 300 3D timelapse datasets
- fully automated
- "mitotic" events detected in low-resultion image
- 3D stacks using high-resolution water immersion

For fun I tried to install @python.org and @napari.org and @pycharm.dev on a chromebook to see if my experimental plugin to view CZI file incl. metadata also would run ...

... and it works :-)

It is Friday again and here is a video on our new AI-assisted labeling tool (SAM-based) on arivis AI (www.apeer.com) from #zeiss_micro.

It makes partial labeling to train your models (semantic or instance) even faster. The 1st cell is still annotated the usual way, the others using the new tool.

Hi all,

sometimes on Fridays I find some time to play around with some of our new features from ZEN software from #zeiss_micro.

Here a demo of using the PixelStream (via ZEN API) to directly "segment" the acquired images by applying an ONNX model to the pixel stream.

Hello Feedback Microscopy 😁!

I finally found some time to play around with @marimo.io notebooks (really cool) and my little python project github.com/sebi06/czito....

Here you can see it in action 😜