Plate Editor
This standalone software is installed with the control software and allows creation of custom plates which can later be used in the control software.
Overview
The software is split into three main areas:
Logical plate structure
This area displays the hierarchical plate structure and supports addition and deletion of layers, shapes and points. The corresponding buttons always affect the currently selected item.
Properties view
This area displays the properties of the item currently selected in the hierarchical plate structure.
Plate preview
This area contains a live preview of the plate structure as seen from top.
Click on the 
icon to get access to view options that control the degree of details displayed.
Plate model
The software uses a hierachical structure to model plates:
- Plate defines the dimensions of the plate.
- Layers defines a Z-level for content
- Shapes defines the area(s) at which a probe can can reach the Z-level defined by the containing layer without colliding with the plate
- Points mark positions within the shape(s) that can be targeted by the control software
- Shapes defines the area(s) at which a probe can can reach the Z-level defined by the containing layer without colliding with the plate
- Layers defines a Z-level for content
Plate
Properties:
| Property Name | Purpose |
|---|---|
| Name | Identifies the plate (will be displayed in the control software) |
| Description | Description of the plate (will be displayed in the control software) |
| X/Y dimension | Length/width of the plate. |
| Height | Height of the plate. |
Layer
Properties:
| Property Name | Purpose |
|---|---|
| Name | Name of the layer |
| Height of content | Height of the layer measured from the plate’s bottom. This should correspond to the bottom of all wells or shapes within the layer. |
Each layer may contain multiple shapes.
Shape
Within each shape, the head may move freely without rising to the travel offset defined in the control software. Typically, on a multiwell plate, a shape corresponds to one well minus a margin that is not reachable by a probe.
To simplify the editing process, shapes can be arranged in a uniform grid.
Properties:
| Property Name | Purpose |
|---|---|
| Name | Name of the shape |
| X/Y offset | Position of the shape’s center relative to the plate’s origin. In case of a shape grid, this corresponds to the center of the pattern’s lower left shape. |
| Type of shape | Defines the geometry of the shape |
| Diameter or X/Y dimension | Define the size of the shape (depending on the shape type) |
| Repetitions in X/Y | The number of rows/columns of shapes in a uniform grid |
| X/Y spacing | The distance between centers of shapes in a uniform grid |
Note
A shape with a X or Y dimension less than 10mm does not support relative positioning in the control software. If the shape does not contain any points, the control software will always navigate the probe to the shape’s center.
Important
All coordinates and positions are tip-centric and must be reachable by the head without collision. The control software does not perform any collision checks.
The dimensions of the head can be found in the sample holder guide to correctly calculate the size of a shape.
Each shape may contain a single grid of points. If shapes are arranged in a grid, each instance of the shape contains identical points.
Points
Points serve as targets within the shape to which the head can be navigated in the control software.
The points can either be
- single points (a single coordinate relative to the containing shape) or a
- list of coordinates which may, for example, model a structure that is placed within a shape and has a set of fixed positions.
The coordinates must be given in form of aCSV-file where- each line contains a pair of X and Y coordinates (in this order), separated by a semicolon
;or a tab space - each coordinate must be given as a integer or decimal number, optionally followed by the unit which may be either of
nm,um/µm,mmorm. If no unit is specified, micrometer (µm) is assumed. E.g.
0um;100um
100um;100um - the origin of the coordinate system coincides with the offset of the point within the shape
- each line contains a pair of X and Y coordinates (in this order), separated by a semicolon
Like shapes, points can be arranged in a uniform grid.
| Property Name | Purpose |
|---|---|
| Name | Name of the point(s) |
| X/Y offset | Position of the point relative to the shape’s origin. In case of a point grid, this corresponds to the position of the pattern’s lower left point. |
| Type of point | Defines the type of points (see above) |
| Repetitions in X/Y | The number of rows/columns of points or point lists in a uniform grid |
| X/Y spacing | The distance between points or (origins of) point lists in a uniform grid |
Positioning
The following conventions apply for positions on the plate:
| Level | Origin | Positioned relative to |
|---|---|---|
| Plate | front left corner at the bottom of the plate | |
| Shape | center of the shape | plate origin |
| Single Points | the point itself | origin of the containing shape |
| List of coordinates | origin of the coordinates | origin of the containing shape |
Grids grow in positive X and Y direction, hence their origin always coincides with the origin of the grid’s front left shape/point.
Restrictions
Plate size: Please refer to the sample holder guide for physical limitations of the plates.
Supported shape geometries: shapes can only be circles or rectangles.
Number of shapes: The total number of shapes (or wells) on the plate is limited to 384.
Intersections: Shapes must be located completely within the plate’s bounds and must not overlap each other; points must no be located outside the shape. The software automatically detects violations of this rule and displays an error message upon violation.
Integrating the plate into the control software
On start, the control software scans a special directory in the file system and loads all plates therein. The plate editor software can save plates directly to this directory, such that they become available when the control software is started the next time.
When saving a new plate, the software will ask you whether to make the plate available in the control software:
The plate will be saved with the displayed name (based on the Name property of the plate) unless a plate with the same name already exists. In this case you will have to provide a different name or overwrite the plate with the same name.
Important
Please double check the plate before choosing this option, as the control software is unable to detect collision risks and may crash the hardware into the plate if the plate is not properly modeled.
Note
The plate location is bound to the user that is running the control software. Therefore the plate editor software will only save plates to the correct location when run by the same user.
After a plate is made available to the control software, it can still be edited by choosing the corresponding option when the plate editor is started. After making changes to such a plate, the control software needs to be restarted before the changes become effective.
Removing a plate from the control software
If a plate should no longer be available, the plate has to be manually removed from the control software’s plate directory. The directory defaults to:
C:\Users\<username>\AppData\Local\Cytosurge\Plates\
where <username> is the username of the account used to run the control software.
Example: Creating a 24-well plate step by step
Open the plate editor and create a new plate.
Name and describe the plate appropriatley. We measured the plate to be 20.3mm high.
Add a layer to the plate. Its content height is at 3.5mm.
Next, add a shape to respresent the wells to the layer.
The wells are evenly distributed over the plate and always the same size. We can just add one circle und let it repeat over its x and y-axis. The diameter of the wells is actually 16mm but because we only model the tip-reachable part of a well, we subtract 11mm to be safe.
This plate does not provide any predefined points.
Once we are sure that the plate is correct, we can save it via File - Save As … to make it available in the control software.
