Bsoft: Bshow Particle Picking

To activate particle picking, select the "Micrograph/Pick particles" menu item or the boxing tool (square and circle icon). A window will open with a "Boxes" menu and a listing of parameters in a window:

Boxes:
- Delete all boxes - delete all boxes in memory (no recovery!).
- Pick particles - automatically pick particles (uses the "Particle radius", "Particle edge" and "CC threshold" parameters).
- Extract particles - extracts the picked particles to a multi-image file.
- Close - close window and deactivate particle picking.
Parameters:
- Box radius - circle radius around picked particles.
- Bad radius - circle radius for bad regions.
- Particles picked - counts particles picked (not modifyable).
- Bad regions - counts bad regions (not modifyable).
- Radiobuttons to display/hide boxes, labels and bad areas.
- Particle radius - radius of synthetic circular disk used for automatic picking by cross-correlation.
- Particle edge - soft edge width used for automatic picking by cross-correlation.
- CC threshold - threshold in cross-correlation map to pick particles automatically (-1 => threshold set automatically).

To see the particles more clearly at scales below one, select the "Averaging mode". This mode is slow because in displays an average of the data under each pixel rather than just the nearest pixel. The "Pick particles" menu item starts automatic picking, which is based on a crude cross-correlation and may not work in many cases.

Mouse controls for particle picking

Left button: create a box, or move a box or bad circle
Middle button: create a bad circle, or move a box or bad circle
Control - left button: create a bad circle, or move a box or bad circle
Shift - left button: delete a box or bad circle

Clicking the left mouse button in an empty region on the image creates a new selection box. Clicking the left or middle button inside a box allows that box to be moved.

Clicking the middle button in an empty region on the image creates a new "bad" circle. Bad circles are areas that will be deleted when the particles are extracted from the micrograph. On a Mac, pressing the control key and clicking the mouse button have the same effect. Clicking the left or middle button inside a bad circle allows that circle to be moved.

To delete a box or bad circle, hold down the shift key and click the left button inside the box or circle.

The selection boxes are numbered consequtively, so that deleting a box results in all the boxes with larger numbers being renumbered.

Saving and reading particle coordinates

The "Micrograph/Read parameters" and "Micrograph/Write parameters" menu items of the main Bshow window are used to read and write parameter files (usually in the STAR format).

Bshow Particle Picking

Version 1.5.4

Mouse controls for particle picking

Saving and reading particle coordinates