Define Grid produces a grid of desired specifications either manually, or automatically based on previously identified objects.
This module defines the location of a grid that can be used by modules downstream. You can use it in combination with
IdentifyObjectsInGrid to measure the size, shape, intensity and texture of each object or location in a grid. The grid is defined by the location of marker spots (control spots), which are either indicated manually or found automatically using previous modules in the pipeline. You can then use the grid to make measurements (using
IdentifyObjectsInGrid). Text annotation of a grid can be shown on top of an image using the
DisplayGridInfo module (coming soon).
If you are using images of plastic plates, it may be useful to precede this module with an IdentifyPrimaryObjects module to find the plastic plate, followed by a Crop module to remove the plastic edges of the plate, so that the grid can be defined within the smooth portion of the plate only. If the plates are not centered in exactly the same position from one image to the next, this allows the plates to be identified automatically and then cropped so that the interior of the plates, upon which the grids will be defined, are always in precise alignment with each other.
Available measurements
- Rows, Columns: The number of rows and columns in the grid
- XSpacing, YSpacing: The spacing in X and Y of the grid elements.
- XLocationOfLowestXSpot: The X coordinate location of the lowest spot on the X-axis.
- YLocationOfLowestYSpot: The Y coordinate location of the lowest spot on the Y-axis.
See also IdentifyObjectsInGrid.
Settings:
Name the grid
This is the name of the grid. You can use this name to
retrieve the grid in subsequent modules.
Location of the first spot
Grid cells are numbered consecutively; this option identifies the
origin for the numbering system and the direction for numbering.
For instance, if you choose Top left, the top left cell is
cell #1 and cells to the right and bottom are indexed with
larger numbers.
Order of the spots
Grid cells can either be numbered by rows, then columns or by
columns, then rows. For instance, you might ask to start numbering
a 96-well plate at the top left (by specifying the location of the first spot).
- Rows: This option will give well A01
the index 1, B01 the index 2, and so on up to H01 which
receives the index 8. Well A02 will be assigned the index
9.
- Columns: With this option, the well A02 will be assigned
2, well A12 will be assigned 12 and well B01 will be assigned
13.
Define a grid for which cycle?
The setting allows you choose when you want to define a new grid:
- Once: If all of your images are perfectly aligned with each
other (due to very consistent image acquisition, consistent
grid location within the plate, and/or automatic cropping
precisely within each plate), you can define the location of the
marker spots once for all of the image cycles.
- Each cycle: If the location of the grid will vary from one image cycle
to the next then you should define the location of the marker spots
for each cycle independently.
Select the method to define the grid
Select whether you would like to define the grid automatically (based on objects
you have identified in a previous module) or manually. This setting
controls how the grid is defined:
- Manual: In manual mode, you manually indicate
known locations of marker spots in the grid and have the rest of
the positions calculated from those marks, no matter what the
image itself looks like. You can define the grid either by
clicking on the image with a mouse or by entering coordinates.
- Automatic: If you would like the grid to be defined
automatically, an IdentifyPrimaryObjects module must be run prior to
this module to identify the objects which will be used to define
the grid. The left-most, right-most, top-most, and bottom-most
object will be used to define the edges of the grid, and the rows
and columns will be evenly spaced between these edges. Note that
Automatic mode requires that the incoming objects are nicely
defined: for example, if there is an object at the edge of the
images that is not really an object that ought to be in the grid,
a skewed grid will result. You might wish to use a
FilterObjects module to clean up badly
identified objects prior to defining the grid. If the spots are
slightly out of alignment with each other from one image cycle to
the next, this allows the identification to be a bit flexible and
adapt to the real location of the spots.
Select the previously identified objects
(Used only if you selected Automatic to define the grid)
Select the previously identified objects you want to use to
define the grid. Use this setting to specify the name of the objects that will
be used to define the grid.
Select the method to define the grid manually
(Used only if you selected Manual to define the grid)
Specify whether you want to define the grid using the mouse or by entering
the coordinates of the cells.
- Mouse: The user interface displays the image you specify.
You will be asked to click in the center of two of
the grid cells and specify the row and column for each. The
grid coordinates will be computed from this information.
- Coordinates: Enter the X and Y
coordinates of the grid cells directly. You can display an image
of your grid to find the locations of the centers of the cells,
then enter the X and Y position and cell coordinates for each
of two cells.
Select the image to display
(Used only if you selected Manual + Mouse to define the grid)
Specify the image you want to display when defining the grid.
This setting lets you choose the image to display
in the grid definition user interface.
Coordinates of the first cell
(Used only if you selected Manual + Coordinates to define the grid)
Enter the coordinates of the first cell on your grid.
This setting defines the location of the first of
two cells in your grid. You should enter the coordinates of
the center of the cell. You can display an image of your grid
and use the pixel coordinate display to determine the
coordinates of the center of your cell.
Row number of the first cell
(Used only if you selected Manual + Coordinates to define the grid)
Enter the row index for the first cell here. Rows are
numbered starting at the origin. For instance, if you chose
Top left as your origin, well A01 will be row number 1
and H01 will be row number 8. If you chose Bottom left,
A01 will be row number 8 and H01 will be row number 12.
Column number of the first cell
(Used only if you selected Manual + Coordinates to define the grid)
Enter the column index for the first cell here. Columns
are numbered starting at the origin. For instance, if you chose
Top left as your origin, well A01 will be column number 1
and A12 will be column number 12. If you chose Top right,
A01 and A12 will be 12 and 1, respectively.
Coordinates of the second cell
(Used only if you selected Manual + Coordinates to define the grid)
This setting defines the location of the second of
two cells in your grid. You should enter the coordinates of
the center of the cell. You can display an image of your grid
and use use the pixel coordinate display to determine the
coordinates of the center of your cell.
Row number of the second cell
(Used only if you selected Manual + Coordinates to define the grid)
Enter the row index for the second cell here. Rows are
numbered starting at the origin. For instance, if you chose
Top left as your origin, well A01 will be row number 1
and H01 will be row number 8. If you chose Bottom left,
A01 will be row number 8 and H01 will be row number 12.
Column number of the second cell
(Used only if you selected Manual + Coordinates to define the grid)
Enter the column index for the second cell here. Columns
are numbered starting at the origin. For instance, if you chose
Top left as your origin, well A01 will be column number 1
and A12 will be column number 12. If you chose Top right,
A01 and A12 will be 12 and 1, respectively.
Retain an image of the grid?
Select Yes to retain an image of the grid for use later in the pipeline.
This module can create an annotated image of the grid
that can be saved using the SaveImages module.
Name the output image
(Used only if retaining an image of the grid for use later in the pipeline)
Enter the name you want to use for the output image. You can
save this image using the SaveImages module.
Select the image on which to display the grid
(Used only if saving an image of the grid)
Enter the name of the image that should be used as
the background for annotations (grid lines and grid indexes).
This image will be used for the figure and for the saved image.
Use a previous grid if gridding fails?
If the gridding fails, this setting allows you to control how the module responds
to the error:
- No: The module will stop the pipeline if gridding fails.
- Use any previous grid:: The module will use the
the most recent successful gridding.
- Use the first cycle's grid: The module will use the first gridding.
Note that the pipeline will stop in all cases if gridding fails on the first image.