in case you want to learn how to use image analysis to automate your microscope the following webinar might be the right one for you:
Guided Acquisition (paid version) is a dedicated software module of ZEN blue but also can be used via a scripted version. In principle it uses your image analysis to automatically acquire predefined experiments on region identified by the image analysis. The webinar will focus on the paid software module mainly.
- the module will use ZEN image analysis pipelines to detect such regions using:
- classical segmentation and analysis pipelines
- machine-learning segmentation via Intellesis
- it also allows to use your own trained networks for segmentation imported in ZEN blue
For those interested in how to integrate your custom image segmentation pipeline the scripted version might be right too for you. This approach also allows to integrate any image analysis (via APEER modules or by calling external scripts directly from within ZEN) to find the objects of interest.
The cool things is that ZEN blue 3.2 now supports running docker containers integrated in ZEN with a user-definable interface from within its scripting engine. (Some of you might remember my talk and workshop at the NEUBIAS 2020 …
- use Fiji macros or scripts to detect you region of interest
- use python libraries (scikit-image, opencv, …) to find what you are looking for
For more detailed information on Guided Acquistion and on how to customize such workflows visit the Guided Acquisition section on the github page.
Below some example application acquired on the Celldiscoverer 7 system.