Working with Image Sets

Image-Pro allows you to open and navigate multi-frame, multi-dimensional image sets that are saved in a compatible image set file format (such as the OME TIF format). If you open an image set, the image window is configured with special controls that allow you to navigate the various dimensions of the set.

The image set toolbar can be found at the bottom of the image window.

At the bottom of the viewer, Image-Pro provides sequence controls for each dimension of the image set. For example, a set with more than one channel, more than one time point (giving it a time dimension) and more than one Z plane, giving it a Z dimension would have three controls, one for each of these dimensions.

Note: If all elements of a dimension are being simultaneously displayed in the viewer, then the sequence control for that dimension is grayed out. This is the case with the Channel dimension when a set is being displayed in the composite view (where all channels are displayed simultaneously). Another example would be when you view a set in 3D viewer mode. In this case, all images of the Z-stack are being viewed simultaneously so the "Z" dimension sequence controls are grayed out.

You can use the controls at the bottom of the viewer to:

Navigate to different instances of the image set.
"Play" the sequence for a selected instance of a single dimension. Play controls are applied to the Active dimension, which is highlighted on the left side of the sequence tools.
Extract a one-dimensional sequence from the image set to a separate image sequence file (the active dimension is extracted).
Toggle between color composite and single-channel views of the image set.

Standard image editing and image analysis operations can be done on image sets, such as the following:

Cropping
3D Count/Size
Annotations
Applying 2D and 3D Filters

Note: If a tool cannot be used with image sets, it will be grayed out in the ribbon bar.

When an image set has multiple sites, which have names matching the multi-well plate naming convention (e.g. A01, B10, D12,...) , the Plate Viewer will be automatically shown in a separate panel. The plate viewer shows the name of each row (as a letter) and each column (as a number), populated wells are displayed in blue, empty wells are displayed in gray, and the currently selected well is displayed in red. Change the selected well by clicking on any well which is displayed in blue. The active image will be updated, and the selected well will change to red on the Plate Viewer.

You can set an active range of wells using the Plate Viewer. The active range will be applied for processing, such as the application of filters, or for analysis with Protocols. The active range can be selected by clicking and dragging an area that includes your wells of interest. Wells included in your active range are displayed in blue, whilst those wells which are outside of the active range are displayed in pale blue. You can click on column or row headers to add full rows or columns to the active range, doing this with the CTRL key selected adds the row or column to the currently selected active range. The active range can be reset by clicking the top-left corner of the Plate Viewer.

Select the top left-hand corner of the plate viewer to reset the active range to include the whole plate.

Well Plate Actions

Action	Result
Click on a Well	Change the Active Well to the clicked well. The active image will update, and the well is colored red.
Drag to select a group of wells	The selected wells will be set to the ‘Active Range’
Click on a Row or Column Header	Set the Row or Column to the ‘Active Range’
Click on a Row or Column Header with CTRL key pressed	Add the Row or Column to the ‘Active Range’
Click in the top left corner	Reset the ‘Active Range’ to include all populated wells.

Alternatively, the active range for any dimension can be set by dragging the calliper markers from both sides of the navigation toolbar (which is located beneath the image) or using mouse clicks in combination with Shift and Ctrl keys:

Shift – Click – select the range from the active location to the click location.

Ctrl – Click – toggle the clicked location.

Ctrl – Shift - Click – toggle the range from the active location to the click location. Using the <Ctrl> key the active range can be defined as multiple discontinues locations.

Double Click – resets the active range (the active range for a dimension can also be reset clicking the Reset button on the left hand side of the toolbar).

The plate map can be used for following purposes:

Navigation: You can easily move from well to well and view the images.
Selection: Set active range of wells for processing.

The Active Range is supported these modes of operation:

Deconvolution: All selected wells selected will be deconvolved.
Image processing: 2D and 3D filters will be applied to the active range. B, G and C along with B&W settings and other image normalization processing will be applied to active range.
Crop : A duplicate set containing only the active range is generated.
Protocols: Executed on the active range. A heat map can be generated in the same well format.

The visibility of the Plate Viewer can be toggled using the Plate Viewer button, which is found in the image set navigation toolbar. This button is only visible for well based image sets.