icon to display the Design/Run Experiment window.1. From the Resolve3D
window, click the Experiment
icon to display the Design/Run Experiment window.
2. Click the Design tab.
3. Set up Z sectioning and channels as usual. In a plate scan, the first channel is always used for Autofocus. The experiment design elements of Time Lapse, Points, Panels, and Actions are incompatible with Plate Scanning. These features are not used in this process.
4. Select the Plate tab and activate the Do Microtiter Plate Scanning check box.
5. In the Rows of panels per well and Columns of panels per well fields, specify the number of rows and columns of panels to be used to sample each well’s contents. Keep in mind that using large numbers of panels can generate huge amounts of data.
6. In the Panel Separation field, specify the distance for panel separation. The single value is used for both horizontal and vertical separation of panels.
7. In the Panel Scan Pattern field, select Serpentine or Raster.
The Serpentine panel scan pattern is bi-directional.
The Raster panel scan pattern is unidirectional.
The length of time it takes to perform a Serpentine scan is less than the length of time for performing a Raster scan. This is because, with a raster scan, the microtiter stage must return to the beginning of each row of panels to start the next row. However, due to the unavoidable hysteresis involved with the bi-directional Serpentine scan, a Raster scan will always be the more accurate.
8. In the Autofocus Method field, choose an appropriate Autofocus model to use for this acquisition. The options for this field are as follows:
a. UltimateFocus (Hardware) - Use this feature to help maintain focus within a specific move threshold. You can use UltimateFocus either while exploring a sample, or when collecting experimental data.
b. Image Contrast (Software) – This method uses the software autofocus feature to focus the sample..
c. Both – The UltimateFocus and then Image Contrast autofocus methods are used.
9. In the Autofocus Frequency field, choose an appropriate Autofocus model to use for this acquisition. The options for this field are as follows:
a. Once Per Well – Autofocus is used on the first panel within each well.
b. Each Panel – Autofocus is used on every panel in every selected well.
If you would like to modify the Autofocus search parameters, click the More Settings button located next to the Autofocus Frequency drop-down list. The “long” range is used when doing the Once Per Well model or on the first panel of an Each Panel Autofocus style. The “short” range is used when focusing on each panel within a well. These values will be remembered and are not part of the experiment macro.
10. Use the Plate View
window to make a selection of wells to scan. From the Plate View window,
select the 
icon to change to
Select mode.
11. With the mouse, click
and drag an outlined region to select a group of wells on the plate. Click
and drag while holding the Shift
key down to extend the selection or to de-select specific wells. You can
use the Undo 
icon to undo one level of changes to the well selection list. The selected
wells are highlighted in the Plate View window.
Alternatively, you can click on the row letters or column numbers to select
the entire row or column. Use this method in combination with the Shift key to select multiple rows
or columns (or rows and columns).
12. When you are satisfied
with the well selection, click the Visit
icon and click on the top left well in your selected
list.
13. Bring this well into focus to set the best Z estimate for the start of the scan.
14. In the Plate View
window, click Generate Plate Point List
to apply your well selection list. You can check your point list by selecting
the Marked Points List 
icon in the Resolve3D window. The Point List window is displayed. Notice
that the points are labeled with the Well Row/Column specification.
15. Return to the Design/Run Experiment tool and save the experiment.
Note: The saved Experiment Macro tells the system how you want the well scanning to be done. The Plate Point List tells the system what you want to scan. Since the Experiment Macro and the Plate Point List are relatively independent from one another, you can re-use the Experiment macro with a different list of selected wells, or you could re-use the list of selected wells and perform multiple styles of imaging on the same list. |
Selecting and Deselecting Wells