Many neuroimaging applications involve the use of multiple fluorescent indicators, serving to provide valuable contrast to the experimenter during live imaging.
ScanImage 3.5 allows the image data from the (up to 3) detection channels to be combined into an 8-bit RGB image which is updated live during image acquisition. This RGB Channel Merge figure can be enabled in the Channels... dialog box accessed via Settings >> Channels... from the Main Controls window menubar:
New Controls
- Enable: Selecting this checkbox opens the RGB Merge Figure. The other checkboxes are only active if this is selected.
- FOCUS only?: Selecting this option specifies that the display in the RGB Merge Figure is only updated during FOCUS acquisitions. Most applications requiring live display are done using FOCUS mode (e.g., focusing or translating the specimen, targeting a micropipette, etc). Because GRAB/LOOP acquisitions can require extra processing in the data stream, e.g. for disk logging, some users/computers may find it appropriate to not expend computing power to compute/display the RGB merge display during GRAB/LOOP acquisitions.
- Blue->Gray: Selecting this checkbox causes Channel 3 data to be displayed as gray, rather than blue, which may improve visibility for some monitors and/or users.
Usage Notes
A typical application of the Live RGB Channel Merge display is for targeting a micropipette filled with red indicator to a neuron expressing green fluorescent protein.
Image courtesy of Eugenia Chiappe (Jayaraman Lab, HHMI/Janelia Farm)
Note that channel 1 is green; channel 2 is red; channel 3 is blue or gray (depending on Blue->Gray checkbox in Channels dialog box).
The intensity of each color in Merge figure is determined by the LUT values employed for that channel.
This figure is like the other acquisition and max projection figures: its position, size, etc. are stored as part of the user settings.