CHANNELS Dialog
The Channels dialog – accessed from
on the Main Controls panel menubar – controls various settings related to handling of ScanImage's up to 4 input Channels. This dialog is modal meaning that it must be closed before ScanImage (or any Matlab) operation can continue. When the dialog is closed, any changes made take effect.
The settings controlled on this dialog are all part of either the ScanImage Configuration or the ScanImage User Settings.
The
and
buttons cause the (corresponding) values set on this dialog to be saved to the active CFG and USR files, respectively.
Channel Configuration Settings
These settings are all part of the ScanImage Configuration. The values selected can be saved to the active CFG file by pressing
- Unknown macro: {blue}: Specifies which of the up to 4 input Channels are enabled, implying that corresponding Analog Input physical channel will be activated during acquisitions and the incoming data will be processed by ScanImage.
When a Channel is disabled, all other settings for that Channel number are disabled or ignored.
- Unknown macro: {blue}: Specifies which of the enabled Channels will have data saved to image file during or after acquisition.
This setting applies regardless of which of the three methods of file saving are used
Disabling
Unknown macro: {blue}for a Channel is primarily useful for reducing size of stored files, if Channel data need not be recalled
Disabling
Unknown macro: {blue}for a Channel also reduces stripe processing time, but effect is often small
- Unknown macro: {blue}: Specifies which of the acquiring Channels will have input data update their respective image display figures during acquisition. The Channel's image display figure will be shown/hidden accordingly, upon closing the CHANNELS... dialog.
Disabling
Unknown macro: {blue}for one or more Channel(s) often significantly reduces stripe processing time, while still allowing data to be saved to disk (viaUnknown macro: {blue}).
- Unknown macro: {blue}: Specifies for which of the acquiring Channel(s) a maximum projection image will be displayed and updated by the most recent acquisition.
This feature is particularly useful when collecting Image Stack acquisitions
- Unknown macro: {blue}: Specifies bipolar voltage range used by Channel's physical Analog Input channel when digitizing input data, i.e. value of 10 or -10 implies a voltage range of (-10 - 10 V) is used. Note that ScanImage only uses half the bipolar range; the sign of theUnknown macro: {blue}value determines which half is used, i.e. 0-10V or -10-0V for 10 and -10, respectively.
See Input Conditioning and Digitization for more details
Choosing a negative range effectively inverts a negative input signal
- Unknown macro: {blue}: Specifies what 'false' color, if any, to assign to acquired data for particular Channel on the Channel Merge Display, if enabled (Unknown macro: {blue}– see below). Options are 'Red', 'Green', 'Blue', 'Gray', and 'Omit'.
The 'Gray' option is provided as it is often easier to visualize than 'Blue'
If more than one Channel is assigned to the same color, the pixel values for each are summed after each is individually normalized by the Channel
Unknown macro: {blue}values (see Image Controls). See Image Display Figures.
Channel Merge Display Settings
These settings are all part of the ScanImage User Settings. The values selected can be saved to the active USR file by pressing
- Unknown macro: {blue}: Specifies, if enabled, that live Channel Merge Display will be displayed and updated during acquisition, providing a single live false-color image of acquired data.
When scanning at very fast rates and requiring the Channel Merge Display, it can make sense to disable the individual Channel image figures (i.e. disable
Unknown macro: {blue}), to reduce the number of image figures that must be updated live during acquisition.
- Unknown macro: {blue}: Specifies, if enabled (default), that Channel Merge Display will only be updated during FOCUS mode acquisitions, i.e. will not be updated during GRAB or LOOP acquisitions.
PMT Offset Settings
- Unknown macro: {blue}: (Read-Only) Indicates last-measured PMT Offset value for each input channel, in volts
- Unknown macro: {blue}: (Unlabeled) If checkbox is selected, the offset value for Channel N is automatically subtracted from displayed and stored image data for that channel.
- Unknown macro: {blue}: Initiates a manual readout of PMT offset value, updating the stored PMT offset value for each of the input channels.
- Unknown macro: {blue}: If selected, the PMT offset values are measured and updated at the start of each acquisition (FOCUS, GRAB, or LOOP).
See Image Controls
The PMT Offset commands on this panel can also be accessed from the Image Controls panel
Channel Colormap Settings
- {blue:Colormap}
These controls should contain evaluable Matlab expressions, i.e. either a Matlab built-in function or a user-created function (on the Matlab path). The evaluable expression should generate an Nx3 matrix as described in the Matlab colormap documentation
.
By default, the function scim_colorMap() is used, which is available as part of the ScanImage installation in the scim directory.
The selection of a
on the Image Controls panel is effectively just a macro to update the arguments to scim_colorMap() entered in the Channels... dialog
scim_colorMap()
The scim_colorMap() function contains three arguments – mapType, resolutionBits, and saturationPercentage:
- mapType: String specifying which of the ScanImage built-in colormap options. These are described in the IMAGE CONTROLS documentation.
- resolutionBits: (Default=8) Specifies the number (N) of colormap entries to generate (an Nx3 matrix) in terms of a number of bits, i.e. N = 2^(resolutionBits).
- saturationPercentage: (Default=5) Applies when mapType is member of {grayHighSat, grayLowSat, grayBothSat}. Specifies, as a percentage of the range specified by the
Unknown macro: {blue}levels in the Image Controls panel, how close a pixel value to be to either edge to be colored as 'saturated'.
Users requiring their own colormap can use scim_colorMap() as a model for creating a colormap function.
The option exists in these versions to specify that pixels at the high and/or low (within 5%) of the current
and/or
levels, respectively, using the Settings >> Colormap options on the MAIN CONTROLS panel.