Cropping Shade Corrected Movie Process Description

Cropping Shade Corrected Movie Process Description:

This process can be used to crop shade corrected images from step 2 for selected channels of the movie. This is an optional process but can be used in situations where there are multiple cells in the image, and you are only interested in analyzing one cell or a region of a cell. The cropped shade corrected images will be used for the later steps.

Parameter Descriptions:

Input Channels:

This allows you to select which channels you want to crop shade corrected images. This should be applied to all channels that are going to be used for ratioing or bleedthrough correction. Select the channels by clicking on them in the "Available Input Channels" box and then clicking "Select->" to move them to the "Selected Channels" box. You can unselect a channel by clicking the "Delete" button.

Select region of interest for cropping:

If this box is checked, another figure will pop up and display the “current image” with a blue rectangle box around the edges of the image. You can adjust the “blue box” from the edges to the region you are interested in cropping. Once you are happy with the region you selected, you can go back to the “Setting” GUI and click “Crop movie”. This will close the “current image” figure and put the calculated position values in the “Crop ROI positions” box.

Current image:

This allows you to select the number of image to be displayed in the “current image” figure. You can either select by manually putting the number in the box or by adjusting the sliding bar.

Crop ROI positions [Xmin Ymin Width Height]:

This allows you to manually put the positions of the region of interest (ROI) for cropping, in the format of a 4-element numeric vector of [Xmin Ymin Width Height]. This can also be automatically calculated using the “Select region of interest for cropping” option.

Crop movie:

This button works when the “Select region of interest for cropping” box is checked, and an ROI has been selected using the “blue box” on the “current image” figure. By pressing this button, the “current image” figure will be closed and “Crop ROI positions” will be calculated.