New AI-based quick segment tool in WEBKNOSSOS

We are excited to announce the integration of Meta’s new AI model, SAM: Segment Anything, into WEBKNOSSOS. Designed with flexibility and seamless integration in mind, SAM is a great tool for various applications: cell segmentation, for example, is a great use case for this model.

With the integration of SAM into WEBKNOSSOS, we have enhanced our quick-select tool by introducing an AI option. The AI option will allow you to segment more complex cells, like those containing mitochondria, with greater accuracy.

Example of a few cells segmented with the new AI option in WEBKNOSSOS.

To access the AI option in quick-select, simply click the ‘AI’ button located near the interpolation tool, which will activate the AI mode. Then, like for the traditional quick-select tool, you just need to draw a rectangle around the area you want to segment.

Choosing the AI option of the quick-select tool and annotating a cell.

Quick tip: When dealing with long and complex shapes, try drawing multiple rectangles on different areas. The annotations will merge and your complex shape will be segmented in no time.

Example of segmenting a cell with a long and thin shape. Quick-selecting smaller regions to reach an accurate segmentation.

Speed up your annotation workflow by combining the quick-select tool with the interpolation tool. Read more about efficient annotation processes in our tutorial on volume annotations.

Combining the quick-select tool with the interpolation tool for a fast annotation process.

Another advantage of the AI option is its ability to generalize across various microscopy techniques. Regardless of the microscopy method you use, the AI model is capable of accurately segmenting cells, providing you with a versatile solution.

Example of using the quick-select tool in WEBKNOSSOS on a bright-flied microscopy dataset.

Example of using the quick-select tool in WEBKNOSSOS on a confocal microscopy dataset.

We sincerely hope that you will enjoy this powerful new feature. Don’t hesitate to try it out today on webknossos.org! Follow us on Twitter or Mastodon for more updates.