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@YangLiujames
YangLiujames authored Aug 21, 2023
1 parent bb863c2 commit fa4c275
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105 changes: 105 additions & 0 deletions control_code/O1Scan.bsh
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import java.lang.String;
import java.text.DecimalFormat;
import org.micromanager.data.SummaryMetadata;
import org.micromanager.PropertyMaps;

//acquisition parameter
pathRoot = "D:/data/20220803_beads/TTL200_488_o1";
pathPrefix = "galvo_TL200_range40um_step0.4um_100ms_view1_TL0mmclosertoO2";

int num_ch = 1; // real color channel. For interleaved channel acquisition. reduce the step size by n for n-channel imaging. change the step
int num_view = 1;
boolean interleave = false; // multi channel acquisition mode
// size in python code as well.

int nrFrames = 2;
double step = 0.155 * 3; // unit: um 0.310 * 4
double range = 40; // unit: um
double interval = 0; // unit: s
int scanMode = 0; // 0 for raster, 1 for serpantine
double customOffset = 220; // -260; // unit: um, offset between two views for better coverage
// negative value shifts the stage to left to focus more on the right side

// for metadata store
double angle = 45; // inciden angle
double res = 0.219; // xy pixel size, TTL100 0.439, TTL200 0.219, TTL300 0.146, TTL165 0.266

// check channel information is correct
if (num_ch==1){
interleave = true; //making sure that interleave is true for single color imaging
}
if (!interleave && (channels.length != num_ch)) {
print("number of channels is not consistent!");
num_ch = channels.length;
}


// positive offset value, shifting the view2 towards left
double alignmentOffset = 0; // unit: um, offset between two views due to alignment
double galvoOffset = 0; // unit: um, offset between two views due to different galvo values
double offset = alignmentOffset + galvoOffset + customOffset;

//pre-calculate parameters
int nrSlices = range / step;

// reset the scanning range for multi channel imaging
if (nrSlices % num_ch != 0 && interleave) {
nrSlices = nrSlices - nrSlices % num_ch;
range = nrSlices * step;
}
print("number of slices: " + nrSlices);
double exposureMs = mmc.getExposure();
print("exposure time: " + exposureMs);
double speed = step / exposureMs;
DecimalFormat df = new DecimalFormat("#.####");
print("scan range (um): " + range);
//savePath
savePath = pathRoot + "/" + pathPrefix;
savePath = mm.data().getUniqueSaveDirectory(savePath);

// store data
store = mm.data().createMultipageTIFFDatastore(savePath, true, true);
mm.displays().createDisplay(store);

// SummaryMetadata
summary = mm.data().getSummaryMetadataBuilder();
summary.channelGroup("Channels");
String[] axisOrder = {"z", "channel", "time", "position"};
summary.axisOrder(axisOrder);
coorbuilder = mm.data().getCoordsBuilder().time(nrFrames).stagePosition(1).z(nrSlices).channel(num_view * num_ch);
summary.intendedDimensions(coorbuilder.build());
summary.zStepUm(step*num_ch); // real step in multicolor imaging is step * num_ch
myPropertyMap = PropertyMaps.builder().putInteger("angle", angle).putDouble("res", res).putInteger("view", num_view).putInteger("channel", num_ch).putInteger("pos", 1).build();
summary.userData(myPropertyMap);
store.setSummaryMetadata(summary.build());

// start acquistion
for (int f=0; f<nrFrames; f++){
for(int ch=0; ch<num_view; ch++){
mmc.startSequenceAcquisition(nrSlices, 0, true);
builder = mm.data().getCoordsBuilder().z(0).channel(0).stagePosition(0);

slice=0;

while (mmc.getRemainingImageCount() > 0 || mmc.isSequenceRunning(mmc.getCameraDevice())) {
if (mmc.getRemainingImageCount() > 0) {

tagged = mmc.popNextTaggedImage();
image = mm.data().convertTaggedImage(tagged,builder.time(f).channel(ch).z(slice).build(), null);
store.putImage(image);
slice++;
}
else {
// Wait for another image to arrive.
mmc.sleep(Math.min(.5 * exposureMs, 20));
}
}
mmc.stopSequenceAcquisition();

mmc.sleep(Math.max(200, interval * 1000)); //wait until stage is back to original position
}

}

mm.displays().manage(store);

13 changes: 13 additions & 0 deletions control_code/ROI.bsh
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// roi format: (x0, y0, x_len, y_len)
int x_len = 2048; // desired x widht
int y_len = 1024; // desired y widht
//int y_len = 1300; // desired y widht

int x_lim = 2048; //max pixel along x
int y_lim = 2048; //max pixel along y

int x0 = (x_lim - x_len) / 2;
int y0 = (y_lim - y_len) / 2;

mmc.setROI(x0, y0, x_len, y_len);
print(mmc.getROI());
174 changes: 174 additions & 0 deletions control_code/stageScan_multiPos.bsh
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import java.lang.String;
import java.text.DecimalFormat;
import org.micromanager.data.SummaryMetadata;
import org.micromanager.PropertyMaps;

//acquisition parameter
pathRoot = "D:/data/20210506_xiang";
pathPrefix = "stage_TL100_range500um_step0.31_4um_30ms_view2_interval_2s_488_20mW_561_10mW_1800tp_3pos";
int num_ch = 2; // real color channel. For interleaved channel acquisition. reduce the step size by n for n-channel imaging. change the step
int num_view = 1;
// size in python code as well.

int nrFrames = 1000;
double step = 0.310 * 2; // unit: um
// for 0.219 um/pixel, we can have 0.3097 * n as step size, res
double range = 500; // unit: um
double interval = 60 * 4; // unit: s
int scanMode = 0; // 0 for raster, 1 for serpantine
double customOffset = 0; // -260; // unit: um, offset between two views for better coverage
// negative value shifts the stage to left to focus more on the right side

int nrChannels = num_view; // channels include view and channel, todo, add options for sequential channel imaging

// for metadata store
double angle = 45; // inciden angle
double res = 0.439; // xy pixel size
//double res = 0.219; // xy pixel size


// positive offset value, shifting the view2 towards left
double alignmentOffset = 0; // unit: um, offset between two views due to alignment
double galvoOffset = 0; // unit: um, offset between two views due to different galvo values
double offset = alignmentOffset + galvoOffset + customOffset;

//pre-calculate parameters
int nrSlices = range / step;

// reset the scanning range for multi channel imaging
if (nrSlices % num_ch != 0) {
nrSlices = nrSlices - nrSlices % num_ch;
range = nrSlices * step;
}

print("number of slices: " + nrSlices);
double exposureMs = mmc.getExposure();
print("exposure time: " + exposureMs);
port = "COM4";
double speed = step / exposureMs;
DecimalFormat df = new DecimalFormat("#.####");
print("scan range (um): " + range);
//savePath
savePath = pathRoot + "/" + pathPrefix;
savePath = mm.data().getUniqueSaveDirectory(savePath);

// store data
store = mm.data().createMultipageTIFFDatastore(savePath, true, true);
mm.displays().createDisplay(store);


// get the mulitple positions
pos = mm.positions();
posList = pos.getPositionList();
numPos = posList.getNumberOfPositions();
print("number of position: " + numPos);
print("number of channel: " + num_ch);
print("number of view: " + num_view);

// SummaryMetadata
summary = mm.data().getSummaryMetadataBuilder();
summary.channelGroup("Channels");
String[] axisOrder = {"z", "channel", "time", "position"};
summary.axisOrder(axisOrder);
coorbuilder = mm.data().getCoordsBuilder().time(nrFrames).z(nrSlices).channel(nrChannels*numPos);
summary.intendedDimensions(coorbuilder.build());
summary.zStepUm(step*num_ch); // real step in multicolor imaging is step * num_ch
myPropertyMap = PropertyMaps.builder().putInteger("angle", angle).putDouble("res", res).putInteger("view", num_view).putInteger("pos", numPos).putInteger("channel", num_ch).build();
summary.userData(myPropertyMap);
store.setSummaryMetadata(summary.build());

// scan mode; 0 for raster, 1 for serpantine
message = "scan f=" + Integer.toString(scanMode);
mmc.setSerialPortCommand(port,message,"\r");
print(message);

//set backlash
message = "backlash x=0.04 y=0.0";
print("set backlash: " + message);
mmc.setSerialPortCommand(port,message,"\r");

//// set current position to zero
//message = "zero";
//mmc.setSerialPortCommand(port,message,"\r");

// Camera trigger settings
mmc.setProperty("HamamatsuHam_DCAM", "TRIGGER SOURCE", "EXTERNAL");
String propTRIG = mmc.getProperty("HamamatsuHam_DCAM", "TRIGGER SOURCE");
print("TRIGGER SOURCE:" + propTRIG);

mmc.setProperty("HamamatsuHam_DCAM", "TRIGGER DELAY", "0.0");
String propTRIG = mmc.getProperty("HamamatsuHam_DCAM", "TRIGGER DELAY");
print("TRIGGER DELAY:" + propTRIG);

// start acquistion
for (int f=0; f<nrFrames; f++){
for (int p=0; p<numPos; p++){
// go to next position, reset the scan parameter
//set default speed
message = "speed x=10 y=10";
print("set speed to scan: " + message);
mmc.setSerialPortCommand(port,message,"\r");

pos = posList.getPosition(p);
double px = pos.getX();
double py = pos.getY();
print("px:" + px);
print("py:" + py);
mmc.setXYPosition(px, py);
mmc.sleep(1000);

message = "scanr x=" + df.format((-px) / 1000) + " y=" + df.format((-px + range) / 1000);
print("scan range: " + message);
mmc.setSerialPortCommand(port,message,"\r");
// mmc.sleep(200);

message = "scanv x=" + df.format((py) / 1000) + " y=" + df.format((py) / 1000);
print("scan range: " + message);
mmc.setSerialPortCommand(port,message,"\r");
// mmc.sleep(200);

for(int ch=0; ch<nrChannels; ch++){
mmc.startSequenceAcquisition(nrSlices, 0, true);
builder = mm.data().getCoordsBuilder().z(0).channel(0).stagePosition(0);

//set speed
message = "speed x=" + df.format(speed);
print("set speed to scan: " + message);
mmc.setSerialPortCommand(port,message,"\r");

// start scan
message = "scan";
mmc.setSerialPortCommand(port,message,"\r");

slice=0;

while (mmc.getRemainingImageCount() > 0 || mmc.isSequenceRunning(mmc.getCameraDevice())) {
if (mmc.getRemainingImageCount() > 0) {

tagged = mmc.popNextTaggedImage();
image = mm.data().convertTaggedImage(tagged,builder.time(f).channel(ch+nrChannels*p).z(slice).build(), null);
store.putImage(image);
slice++;
}
else {
// Wait for another image to arrive.
mmc.sleep(Math.min(.5 * exposureMs, 20));
}
}
mmc.stopSequenceAcquisition();

mmc.sleep(400); //wait until stage is back to original position
}
mmc.sleep(2000); //wait until stage is back to next position
}
mmc.sleep(interval * 1000); //wait until next time point
}

mmc.setProperty("HamamatsuHam_DCAM", "TRIGGER SOURCE", "INTERNAL");

//set default speed
message = "speed x=10 y=10";
mmc.setSerialPortCommand(port,message,"\r");

mm.displays().manage(store);

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