Nessys segmentation viewer/sample



When running Nessys and selecting the image you would like to use as an example to set segmentation parameters with, it would be incredibly useful if there was a feature allowing the selection of the cropped region to include the most appropriate areas of the field of view; in addition perhaps having a quadrant view of multiple images from an experiment would allow the generation of more accurate and generalisable segmentation for example during a timecourse experiment where cells may change density/shape.




Hi @Darren,

Great suggestion thanks!
This is certainly feasible just a question of time as usual. I have created a feature request on the PickCells repository.

Maybe the user could create a ‘patchwork image’ at the start by selecting volumes of interest in multiple images (or time frames) and run the preview on his ‘creation’.

This image should probably have a maximum size though in order to avoid long preview times (which could be increased with a warning message).

Also, it would be easier to implement on the programming side if the volumes are predefined with width, height and depth which are multiples of the final image.

What do you think?


Hi Bill @Ghiomm,

That sounds good. The idea of having a drag and “paint” tool to highlight the region of interest and an adjustable slider setting for the z would be nice to select the volumes to use in preview segmentation. In the preview segmentation pane it may also be good to have the z-stack slider for each preview image given they are likely to be different sizes in the Z.

What might be nice is to have the feature editable, that is, if the user is unsure of the number of images/conditions to include for preview segmentation they can open multiple images to check heuristically how generalisable the segmentation parameters will be and then add those images to the preview pane sequentially. This may be easier, for the user, than pre-defining the number of images in the preview segmentation pane.

Hope this makes sense.