Region Scan overview
The region scan function allows the user to image an area via a
succession of camera snaps that can be tiled together to form a complete image of the region.
The images are automatically acquired once the set region of interest has
been defined.
The user has the option to simply image the area of interest or, in
addition, perform object-finding as the scan progresses. The images
themselves, as well as details of the objects found, can be saved for
later use.
After 'Start' is pressed the software asks for a location and format (ics is recommended)
for the image files to be saved. Output is a set of image files
(ics, tif, etc.), an overview image at reduced resolution and a metadata text file.
overlap
There is an option to specify the amount of overlap between images. The
reason for this is to allow the image tiles to be seamlessly stitched together,
for instance using our Mosaic program (available seperately). The larger the overlap
the easier the stiching is, but the longer the scanning takes.
Another reason for the overlap is related to objectfinding, as follows.
Imagine a succession of images which
side by side give a composite picture of the larger area. If an object
lies on an image edge then part of it will appear in one image and part
in another (or if at a corner, it may appear in 4 separate images).
When object finding is enabled this situation would identify these
parts as separate objects. To correct this, the stage moves so that a
certain degree of overlap exists in adjacent images. Now, an object
which lies on the edge of one image is completely captured in the
neighbouring one (if the degree of overlap is sufficiently large) and
the object-recognition algorithm can uniquely identify it. How much
overlap to use depends on the size of the objects which may be
encountered. The default value is set to 10% of the image dimenstion.
Too high a figure slows down the scan time as more frames are needed to
cover the ROI, whereas too low a figure risks large objects still
hitting the edges of adjacent images. Bear in mind that high power
objectives will generally necessitate a larger overlap.
cell finding
To enable cell-finding ensure the box is checked and press 'Configure'
to bring up the cell-finding
options panel. When all settings are correct 'Start' begins the
scan, and options to pause or abort the scan become available.