Procedure for searching for a region of interest in a sample using microscope image acquisition tools during general chat.
This skill describes how to search for a region of interest (ROI) in a sample using a microscope image acquisition workflow. The goal is to find a field of view (FOV) that contains a requested feature and then center that feature in the FOV.
This skill is intended for general chat usage. It should not assume that the required tools or inputs are already available.
To perform ROI search effectively, you need:
acquire_image: Acquire an image at a specified location and with a specified
field of view.If this tool is unavailable, notify the user that the ROI-search workflow cannot be executed as described and explain what capability is missing.
Before starting the workflow, make sure you have the following information:
If any of this information is missing, ask the user for it before proceeding. Check the tool schema as well, because the exact acquisition arguments may vary across instruments.
Use the following workflow:
Confirm the feature being searched for and the acquisition settings needed to begin the search. In particular, confirm:
Start from one corner of the allowed search range and perform image acquisitions following a snake pattern with constant x and y strides. Use the user-provided or agreed-upon FOV size and step size.
Example snake pattern:
Snake-pattern scan with constant x and y strides
(start at lower-left corner in this example)
y ^
|
| row 4 o ---> o ---> o ---> o
| |
| row 3 o <--- o <--- o <--- o
| |
| row 2 o ---> o ---> o ---> o
| |
| row 1 o <--- o <--- o <--- o
| |
| row 0 o ---> o ---> o ---> o
|
+----------------------------------------> x
x stride = constant horizontal spacing
y stride = constant vertical spacing
After each acquired image, inspect whether the feature appears in the FOV. If not, continue the search systematically. At the beginning, prefer a regular grid-search pattern rather than arbitrary movement.
When the feature begins to appear in the image, refine the search more flexibly. Move the FOV in the direction needed to bring the feature toward the center. For example:
You may temporarily increase the FOV size to inspect a larger area if that helps reacquire or localize the feature, but once the feature is found, return to the target FOV size and acquire a final centered image.
Avoid repeatedly acquiring images at the same or very similar locations. If you find yourself sampling nearly the same location over and over, stop and reconsider the search strategy instead of continuing blindly.
Once the feature of interest is found and centered, report the final FOV coordinates clearly to the user.
(y = ..., x = ...)
format instead of listing unlabeled numbers.The workflow is complete when you have found the requested feature and centered it in the FOV, then reported the final coordinates to the user.