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Positions

This dimension is dedicated to image different XYZ positions from a sample. You can switch from this dimension to the Tiling dimension by the button Switch to Tiling.

positions_dimension

To use the Positions dimension:

  1. Do a Preview of your sample.
  2. Move the stage and the focus to the desired position.
  3. Click on Add position to add the XYZ coordinates in the position list.
  4. Click on the Path button if you need to optimize the stage mouvement when you have multiple positions.
    1. The stage moves following the order in which positions were added. You can view the complete movement path and calculate the total distance traveled. To optimize the path and reduce travel distance, click the Sort button.
    2. Once optimization is complete, click the Back button to return to the position dimension view.

      path_before_after

  5. If necessary use Pattern Detection tool which allows the recognition of patterns from the current live image or from ROI:
    1. Click the Start button located in front of the Pattern Detection section.
    2. Create a new tile to find the pattern. Click on New tiling. Set it up as described in the Tiling dimension.
    3. Select the pattern you wish to detect:
      • Current Live Image: Use the pattern from the live image
      • ROI: Draw an ROI around the specific pattern you want to detect.
    4. Indicate the Correlation Threshold (that mean the percentage of similarity between pattern and other form).
    5. Click on Detect pattern to start the detection.

      pattern_detection

    6. Once it’s done, all patterns recognized are surrounded like ROI. You can select or unselect some ROI by clicking on Select all or Unselect All or by clicking directly on the ROI.
      pattern_detection_roi
    7. Then click on Confirm button and position of each pattern will be registered on the position list.
      pattern_detection_positions_list
  6. Adjust Move Strategy if necessary: When performing a multiposition acquisition with a significant distance between two positions, two options are available for the stage moving between these two positions:
    • Fastest: Move directly from position A to position B;
    • XY Split: Move between 2 positions with small steps. Indicate the step by filing the Step (µm);
  7. Make other adjustments or manipulations if necessary:
    • X-Axis/Y-Axis: Change/adjust position if necessary.
    • Focus or Z-axis: Use the focus value used for the selection of the positions. If the checkbox is not selected, the current focus value of the microscope will be used.
    • Move to: Move the stage to this position.
    • Set: Update coordinate of the position by the actual XYZ position of the system; You can modify the axis (X,Y and focus), apply offset on the axis for all positions or for the selected position by clicking on the . You can select which axis you want to modify by checking it.
      edit_position_2
    • Adjusting Exposure Time by Position: This feature allows you to modify the exposure time for specific positions.


      1. Click the camera icon on the line corresponding to the position where you want to adjust the exposure time.
      2. Check the Custom box to enable exposure time modification.
      3. Update the channel value you wish to adjust. The channel corresponds to the one defined in the channel dimension or if no channel is defined in the dimension, the current channel will be used by default.
      4. Click Apply to confirm your changes.

      When a line has been modified, the camera icon color changes from red to green, indicating that a custom exposure time has been set.



    • : delete this position from the position list.
  8. If you have multiple positions you can create different groups of positions. For this click the gear icon to open the settings menu:
    • Name your group.
    • Indicate the range of the position index that you want to group together.
    • Click on Apply.
    • Repeat those steps if you want to do multiple groups.
    group_position
  9. When all positions are set up, click on Confirm.