Part of the Oxford Instruments Group

Image Processing Preview Mode

In this tutorial you will learn how to use image processing functions in Imaris 9.3.

To start: select an image processing icon which opens the image processing pipeline editor and the image processing preview mode. First, you can adjust the size of your preview by dragging yellow frame corners with left mouse button and moving the field of view with right mouse button. You can zoom in with a scroll. Its size affects speed of refreshing of the preview window. You can also switch between Slice and Volume Preview mode. In the Volume mode you see the projection of entire dataset to a given plane while in the Slice mode you can preview a selected plane.

Within the display adjustment window you see duplicated channels for the image processing preview. If the Display adjustment window is not visible, press Ctrl+D. Channels Can be switched on/off and adjusted individually. You can also choose auto adjust all channels option.

Image processing commands are set up for individual channels in the image processing pipeline editor area on the left side of the screen. Simply select a command from an image processing dropdown menu next to the channel and set the parameters. You can see immediate effects of the image processing command on your data in the preview window.

After setting up the desired parameters you can copy the same settings and apply them to the remaining channels by Left -click the Copy button next to the set channel and then Left-click the Paste button next to the remaining channels. Within the same image processing pipeline you can also add additional image processing operations to the selected channels.

Please note that Imaris ClearView deconvolution mode is set up the same way as other image processing functions. This option requires additional license and will be presented within another tutorial. All image processing functions set up within this pipeline are batchable. When the pipeline is set up, confirm with OK and the full dataset will be processed. Save the image with a new name. Please note that now when you select the new thumbnail in the Arena mode, all image processing functions applied are visible under restore points tab.

Category: Tutorial

Download as pdf