Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision 		Previous revision
Next revision Both sides next revision
docs:mm_dispim_plugin_user_guide [2023/05/31 20:58]
Jon Daniels [Light Sheet Synchronization] added note about Fusion 		docs:mm_dispim_plugin_user_guide [2024/02/21 21:16]
Jon Daniels [Cameras Tab]
Line 126: Line 126:
 ===== Cameras Tab ===== ===== Cameras Tab =====
  
-The Region of Interest and camera triggering mode is specified in the Cameras tab. For Andor Zyla and Hamamatsu Flash4 cameras there is the possibility to have consecutive triggers determine the start and end of a image capture; this is termed respectively “Overlap” and “Synchronous” by the manufacturers but referred to uniformly as “Overlap” in the plugin. Because the image sensor is simultaneously read out and reset to begin the subsequent exposure, the camera overhead time is reduced and it allows for faster camera frame rates.8). The downside is that there can be slight “ghosting” or bleedthrough from frame to frame because the reset isn't quite complete. The same mode is not available with the PCO.edge or Photometrics Prime 95B. However, a new exposure can begin shortly after the readout starts which is a mode we refer to as “Pseudo Overlap”.+The Region of Interest and camera triggering mode is specified in the Cameras tab. For Andor Zyla and Hamamatsu Flash4 cameras there is the possibility to have consecutive triggers determine the start and end of a image capture; this is termed respectively "Overlap" and "Synchronous" by the manufacturers but referred to uniformly as “Overlap” in the plugin. Because the image sensor is simultaneously read out and reset to begin the subsequent exposure, the camera overhead time is reduced and it allows for faster camera frame rates. The downside is that there can be slight "ghosting" or bleedthrough from frame to frame because the reset isn't quite complete. The same mode is not available with the PCO.edge or Photometrics Prime 95B. However, a new exposure can begin shortly after the readout starts which is a mode we refer to as "Pseudo Overlap".  In cases where imaging speed is important it is usually a good idea to select "Overlap" or "Pseudo Overlap" camera modes.
  
 <imgcaption plugin_Cameras| The Cameras panel allows you to set the ROI and the acquisition trigger mode.>{{:docs:um-camerastab.png?600| diSPIM plugin Cameras tab}}</imgcaption> <imgcaption plugin_Cameras| The Cameras panel allows you to set the ROI and the acquisition trigger mode.>{{:docs:um-camerastab.png?600| diSPIM plugin Cameras tab}}</imgcaption>
  
 +==== Simultaneous Cameras ====
 +
 +This option was added so that multiple cameras could be used on the same path, e.g. a single-view SPIM with 4 different cameras to record each camera looking at a different spectral window at the same time.
 +
 +Due to Micro-Manager viewer limitations there are some oddities about this feature's implementation.  In simple cases with only 2 cameras it may be easier to instead use the setting on the Settings tab to record from 2 views simultaneously.  When using "Use simultaneous cameras on Path A" each "channel" in the dataset is a different camera as expected.  However if multiple channels are used also, each channel is assigned a portion of the resulting stack, and furthermore no time points are allowed.  For instance with 2 cameras and 3 sets of lasers and 50 slices in the stack the resulting dataset would have 2 channels and 150 slices.
 ===== Settings Tab ===== ===== Settings Tab =====
  
Line 140: Line 145:
 The scanner (micromirror) drive card has adjustable Bessel output filters to protect the filter from being driven near its mechanical resonance (usually 2 kHz). Settings as high as 0.8 kHz are usually acceptable, and in general the shorter the scan period (and faster frame rates) the more this matters. The scanner (micromirror) drive card has adjustable Bessel output filters to protect the filter from being driven near its mechanical resonance (usually 2 kHz). Settings as high as 0.8 kHz are usually acceptable, and in general the shorter the scan period (and faster frame rates) the more this matters.
  
 +==== Simultaneously acquire from both paths/cameras ====
 +
 +This option was added to enable reflective imaging where cameras on both sides are triggered together (see https://www.nature.com/articles/s41467-017-01250-8).  Both cameras should be wired to the same trigger signal using e.g. a BNC "tee" at the Tiger controller output.
  
 +Note this is similar but distinct from the option to acquire multiple cameras on Path A which is configured on the Cameras tab.  However in many cases either one can functionally be used.
 ===== Acquisition Tab ===== ===== Acquisition Tab =====
  

Trace: