This package implements a simple time-lapse tile scanner for ScanImage.
The package defines a class called tiler that is a wrapper around ScanImage.
Tiler sets up tile coordinates, moves an X/Y stage, and instructs ScanImage to take images.
Image acquisition is performed partly via a ScanImage user-function.
Multiple repeats (called "sections") of the same tile region can be obtained.
This allows for things like time-lapse imaging of morphological changes in large brain slices.
Our approach is useful only for specific cases. For instance, we implemented our own motion control classes for this project as we wanted the sample stage to move indepedently from the ScanImage-controlled stage. This has the disadvantage that you will need to write your own control code if you don't use the PI C-891 motion controller, as we did here. However, it has the advantage that you can set up your system in a very open-ended manner. Also note that some settings (e.g. the imagaing depth) are hard-coded.
>> startTiler
Starting...
Connecting to hardware components:
Setting up axis xAxis on linear stage controller C891 #1
PI_MATLAB_Driver_GCS2 loaded successfully.
Attempting to connect to C-891 with serial number 116010269
Setting up axis yAxis on linear stage controller C891 #2
PI_MATLAB_Driver_GCS2 loaded successfully.
Attempting to connect to C-891 with serial number 116010268
Setting sample name to: sample_17-06-28_175354
X=-0.30, Y=2.30
% Now we attach ScanImage to tiler.
>> scanimage % first start scanimage
>> who
Your variables are:
hSI hSICtl hT
% This step is manual, sorry
>> hT.scanner=SIBT;
>> hT.scanner.parent=hT;
Starting SIBT interface for ScanImage
- Setting fast z waveform type to "step"
- Setting up power/depth correction using Lz=180.
You may change this value in "POWER CONTROLS". (Smaller numbers will increase the power more with depth.)
% Set a 2 by 2 mm area
>> hT.recipe.mosaic.sampleSize.X=2;
>> hT.recipe.mosaic.sampleSize.Y=2;
>> hT.beginTileScanning
Setting up acquisition of sample sample_17-06-28_182233
Starting data acquisition