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Low-Magnification Maps

Introduction

The low-magnification maps section is separated in 3 cards each corresponding to a different magnification level.

  • Atlas (left): The lowest magnification where the squares are identified and selected.
  • Square/Area (center): Magnification where the holes are identified. It corresponds to the Search preset in Serialem.
  • Hole/Target (right): Added in 0.8 This is the medium magnification where the hole coordinates can be refined.

It is only possible to access the upper magnification of an area/target that has been acquired. The can beeasily identified with their green ouline and number.

Clicking on them will open the next magnification images.

Map card

This section aims at describing the general properties of the low-magnification maps cards. They can be divided into 4 sections detailed below.

General options

General options are available ot every magnification levels.

Toggle Legend

Will remove the legend and scale bar from the image to allow clicking items that may be hidden under them.

Download images

Added in 0.8

Dropdown menu to download the image that is shown without the overlay in multiple file format.

Difference between raw and .mrc

The .mrc will be the stiched version of the montaged images like atlases while raw will be the the z-stacked montage that was produced by SerialEM.

Display options

Dropdowns menu to display the results from different algorithms on the map. The options will depend on the protocol and magnification level.

Toggling between display options

Toggle fullscreen

Will pop the map out of its position to occupy a larger fraction of the screen. Press again to bring it back to its original size.

Actions/Interaction menu

The insteractions menu sits under the the general options and the amount of options vary between each mangification level. However, they all share the actions dropdown and the clear selection button.

Target acquisition status

There are a few status that a given target can have which will change it's color. As a rule of thumb a target with its number showing in the corner has an active acquisition status. Then, its color gives an indication of status:

  • Orange: In the acquisition queue or Queued
  • Yellow: Actively being aquired (Started) or pending processing (Acquired).
  • Green: Completed. This means the target has been acquired and can be clicked to access the next magnification.

Selecting an modifying targets

To enable the Action dropdown, at least one target should be selected.

Clicking on the actions button will bring a few options change the label given to a hole and, if the grid status is started, you may also add or remove the target(s) from the acquisition queue depending on its/their status.

Skip an active target

Added in 0.9.2

It is possible to skip a started (yellow) target. This is useful if a bad target was automatically selected or ran into an issue. The Skip will turn the target to a gray color. Checkpoints have been added at which the processing of the target will be stopped and the process will move on the next item. On a run restart, the skipped target will be avoided.

Changing the acquisition status in bulk

To add/remove multiple targets from the queue at once, you need to select targets from only one type of status. For example, select only squares that are not in the queue and remove them all at once and vice versa.

Ensure that the selection is cleared before starting a new selection

It is always preferable to use the Clear Selection button next to the Actions dropdown before starting a new selection to have a clean selection.

Square Maps specific actions

The square maps have extra actions.

Edit targets

Added in 0.9.3

The edit target menu is accessible if a Selector had been selected in the Display options

A pencil icon will appear on the card. Clicking it will bring the Selector Viewer menu.

Selector Viewer

  1. Click on the pencil icon to bring the selector viewer

  2. Edit the values using the slider dials.

    The 3 sample images will update in real time with the value change

  3. Save the changes

    • Save will apply the selector to the current grid.
    • Save to session will apply the values to all the grids in the session. Can be useful for multi-grid sessions but will yield odd results if diffirent mesh types are used.

  4. After saving, you'll have the option to regroup the Beam-image shift grouping and reselect the holes on the entire grid. This will take a few seconds to propagate.

All Holes

These are quick ways to act on every targets without selecting them individually. These bulk actions are convinient mainly for data collection.

  • Queue all holes / Cancel all holes: These allow to either add or remove all the holes from the acquisition queue.
  • Regroup BIS: Usually used after changing the Beam-Image Shift parameters or manually classifying the holes. This will re-rerun the grouping procedure on all holes that are not Active (Yellow) or Completed (Green).

Regroup BIS after changing BIS radius

New Targets

It is possible to add targets to an image. To add new targets, hold Shift and left-click at the location where you wish to add targets. The clicked locations will show as red crosses. At that point, the New Targets dropdown menu will be available with the option to clear the newly clicked positions or permanently add the new locations as holes. Clicking Add targets will add the locations to the database and reload the square image with the new targets as blue circles.

Map Image

This is where the images are displayed and the targets can be selected. The Legend in the top left corner will highlight the targets of a specific class when overing on its name. It can help with locating thte targets.

Timestamp

Located at the footer of the card, it is simply diaplying the acquisition date and time of the image.