ScanImage

https://docs.scanimage.org/
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ScanImage is a software package for controlling laser scanning microscopes on custom-built and...
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### Stack Configuration Example

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/FastZ%2Band%2BStackManager%2BAPI.html

Example MATLAB code configuring a fast volume stack with 50 slices, 2 micron step size, and 10 volumes, then starting acquisition.

```APIDOC
## Stack Configuration Example

### Description
Example MATLAB code configuring a fast volume stack with 50 slices, 2 micron step size, and 10 volumes, then starting acquisition.

### Code
```matlab
% a 100 um fast volume of 50 slices
hSI.hStackManager.enable          = true;
hSI.hStackManager.stackMode       = scanimage.types.StackMode.fast;
hSI.hStackManager.stackActuator   = scanimage.types.StackActuator.fastZ;
hSI.hStackManager.stackDefinition = scanimage.types.StackDefinition.uniform;
hSI.hStackManager.numSlices       = 50;
hSI.hStackManager.stackZStepSize  = 2;
hSI.hStackManager.numVolumes      = 10;

hSI.startGrab();
```
```

--------------------------------

### CycleManager Usage Example

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/TileManager%2Band%2BCycleManager%2BAPI.html

Example code demonstrating how to append an iteration, set its delay, set total cycles, and start the cycle.

```APIDOC
```
hSI.hCycleManager.appendNewIteration();
hSI.hCycleManager.cycleDataGroup.getIterByIdx(1).iterDelay = 5;
hSI.hCycleManager.totalCycles = 3;

hSI.startCycle();
```
```

--------------------------------

### Clone and set up lab repository from official releases

Source: https://docs.scanimage.org/Appendix/Lab%2BUpstream%2BWorkflow.html

Use this in an initial setup when starting fresh from the official 'scanimage-basic-releases' repo (Option A). It clones into 'scanimage-lab', renames the remote to 'upstream', creates a local bare repository as the private remote, pushes the main branch, and creates a 'lab/<labname>/custom' branch. All commands are intended to be run in order.

```bash
# 1. Clone the release repository locally
git clone https://<username>:<token>@gitlab.com/vidriotech/scanimage-basic-releases.git scanimage-lab
cd scanimage-lab

# 2. Rename the remote so 'upstream' refers to the official releases repo
git remote rename origin upstream

# 3. Create a local bare repository to act as your lab's private remote
#    (Choose any path on your machine or shared network drive)
git init --bare /path/to/your/lab-scanimage.git
git remote add origin /path/to/your/lab-scanimage.git

# 4. Push to your local bare repository
git push -u origin main

# 5. Create a branch for your lab's customizations
git checkout -b lab/<labname>/custom
git push -u origin lab/<labname>/custom
```

--------------------------------

### Verify ScanImage installation with 'which scanimage'

Source: https://docs.scanimage.org/Configuration/PC%2BConfig.html

Run in MATLAB command window to verify ScanImage installation path. The output shows the installation directory. Then execute 'scanimage' to start ScanImage.

```matlab
>> which scanimage
   C:\Program Files\Vidrio\SI2019bR0_2020-03-16-151209_4d721e971c
>> scanimage
```

--------------------------------

### Configure logging and start a GRAB acquisition

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/Acquisition%2BControl.html

Configure logging for a GRAB acquisition and start it. The start method returns as soon as the acquisition is armed, not when it finishes; use the acqModeDone user function event to run code on completion.

```matlab
hSI.hChannels.loggingEnable = true;
hSI.hScan2D.logFilePath   = 'C:\data';
hSI.hScan2D.logFileStem   = 'experiment_01';
hSI.hScan2D.logFileCounter = 1;

hSI.startGrab();

```

--------------------------------

### Configure a fast uniform stack and start acquisition

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/FastZ%2Band%2BStackManager%2BAPI.html

Sets up a 100 um fast volume of 50 slices using the StackManager API, then starts acquisition with hSI.startGrab(). The example uses uniform stack definition, fastZ actuator, 2 um step size, and 10 volumes.

```matlab
% a 100 um fast volume of 50 slices
hSI.hStackManager.enable          = true;
hSI.hStackManager.stackMode       = scanimage.types.StackMode.fast;
hSI.hStackManager.stackActuator   = scanimage.types.StackActuator.fastZ;
hSI.hStackManager.stackDefinition = scanimage.types.StackDefinition.uniform;
hSI.hStackManager.numSlices       = 50;
hSI.hStackManager.stackZStepSize  = 2;
hSI.hStackManager.numVolumes      = 10;

hSI.startGrab();

```

--------------------------------

### hSI.startCycle()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/Acquisition%2BControl.html

Starts the acquisition through hSI.hCycleManager.

```APIDOC
## hSI.startCycle()

### Description
Starts the acquisition through hSI.hCycleManager.

### Method
`startCycle()`

### Parameters
None.

### Returns
None.

### Example
```matlab
hSI.startCycle();
```
```

--------------------------------

### hSI.hTileManager Example

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/TileManager%2Band%2BCycleManager%2BAPI.html

Example code showing how to configure and initialize a tile scan.

```APIDOC
## hSI.hTileManager Example

### Description
Example code showing how to configure and initialize a tile scan.

### Code
```matlab
hSI.hTileManager.scanFramesPerTile   = 10;
hSI.hTileManager.scanStageSettleTime = 0.2;
hSI.hTileManager.initTileScanning();
```
```

--------------------------------

### Create DAQ resource with ResourceStore

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/dabs%2BAPI/DAQs%2Band%2BIO.html

Constructs a ResourceStore and retrieves a DAQ resource by name. The example shows how to get a vDAQ0 board and its AO0 channel.

```matlab
hRS  = dabs.resources.ResourceStore();
hDAQ = hRS.filterByName('vDAQ0');
hAO  = hRS.filterByName('/vDAQ0/AO0');

```

--------------------------------

### Coordinate System API Usage Example

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Coordinate%2BSystem%2BAPI/index.html

Example demonstrating how to get the stage position in sample-relative coordinates, transform it to reference space, and plot the coordinate system tree.

```APIDOC
## Coordinate System API Usage Example

### Description
This example shows how to retrieve the stage position in sample-relative coordinates, transform it to reference space, and display the coordinate system tree.

### Code Example
```matlab
% where is the stage, expressed in sample-relative microns?
hPt = hSI.hMotors.getPosition(hSI.hCoordinateSystems.hCSSampleRelative);
disp(hPt.points);

% ... and the same position in reference space (optical degrees / microns)
hPtRef = hPt.transform(hSI.hCoordinateSystems.hCSReference);

% show the whole tree
hSI.hCoordinateSystems.plot();
```
```

--------------------------------

### hSI.startLoop()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/Acquisition%2BControl.html

Starts a LOOP acquisition: `hSI.acqsPerLoop` independently started acquisitions.

```APIDOC
## hSI.startLoop()

### Description
Starts a LOOP acquisition: `hSI.acqsPerLoop` independently started acquisitions.

### Method
`startLoop()`

### Parameters
None.

### Returns
None.

### Example
```matlab
hSI.startLoop();
```
```

--------------------------------

### Configure and start a cycle with hSI.hCycleManager

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/TileManager%2Band%2BCycleManager%2BAPI.html

Appends a new iteration, sets its delay to 5 seconds, sets the total cycle count to 3, and starts the cycle. This example demonstrates the basic workflow for defining and running a cycle.

```matlab
hSI.hCycleManager.appendNewIteration();
hSI.hCycleManager.cycleDataGroup.getIterByIdx(1).iterDelay = 5;
hSI.hCycleManager.totalCycles = 3;

hSI.startCycle();

```

--------------------------------

### Progress Monitoring Example

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/FastZ%2Band%2BStackManager%2BAPI.html

Example MATLAB code adding a listener to the 'slicesDone' property to print progress during stack acquisition.

```APIDOC
## Progress Monitoring Example

### Description
Example MATLAB code adding a listener to the 'slicesDone' property to print progress during stack acquisition.

### Code
```matlab
% follow progress
hL = most.ErrorHandler.addCatchingListener(hSI.hStackManager,'slicesDone','PostSet', ...
     @(varargin)fprintf('slice %d of %d\n', ...
         hSI.hStackManager.slicesDone,hSI.hStackManager.actualNumSlices));
```
```

--------------------------------

### Set up a new lab member's clone

Source: https://docs.scanimage.org/Appendix/Lab%2BUpstream%2BWorkflow.html

Use these commands for a new lab member's first-time setup: clone the private repository, change into the scanimage directory, and check out the lab branch. After this, the member adds the folder to their MATLAB path. Each member maintains their own clone, so modifying source code does not affect other members' running instances.

```bash
# First-time setup for a new lab member:
git clone https://<username>:<token>@gitlab.com/<your-org>/<your-repo>.git scanimage
cd scanimage
git checkout lab/<labname>/custom

```

--------------------------------

### Initialize local bare repository with git init --bare

Source: https://docs.scanimage.org/Appendix/Lab%2BUpstream%2BWorkflow%2BSourceTree.html

Run this command in SourceTree's terminal to create a local bare repository that acts as your lab's private remote. Replace /path/to/your/lab-scanimage.git with the actual folder path, e.g., C:/Users/you/lab-repos/lab-scanimage.git.

```bash
git init --bare /path/to/your/lab-scanimage.git
```

--------------------------------

### hSI.startFocus()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/ScanImage%2BScripting%2BAPI.html

Starts a live view acquisition without logging data. Returns immediately once the acquisition is armed.

```APIDOC
## hSI.startFocus()

### Description
Starts a live view acquisition without logging data. Returns immediately once the acquisition is armed.

### Method
startFocus

### Syntax
hSI.startFocus();

### Parameters
None.

### Return Value
None.
```

--------------------------------

### Start synchronized tasks (ao_task, do_task) in ScanImage

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/vDAQ%2BAPI.html

Starts the ao_task first so it waits for the trigger on D0.0, then starts do_task to wait for the frame clock trigger. The ao_task.start() call automatically starts ai_task because it is synchronized. After ScanImage starts scanning, the frame clock triggers do_task, which then triggers ao_task and ai_task.

```matlab
1% start ao_task first. it will wait for the trigger on D0.0
2ao_task.start();  % automatically starts ai_task since it is synchronized
3
4% then start the do_task which will wait for the frame clock trigger
5do_task.start();
6
7% after ScanImage starts scanning, the frame clock will trigger the do_task,
8% which will then trigger the ao_task and ai_task

```

--------------------------------

### hSI.startGrab()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/ScanImage%2BScripting%2BAPI.html

Starts a single acquisition (grab). Returns immediately once the acquisition is armed.

```APIDOC
## hSI.startGrab()

### Description
Starts a single acquisition (grab). Returns immediately once the acquisition is armed.

### Method
startGrab

### Syntax
hSI.startGrab();

### Parameters
None.

### Return Value
None.
```

--------------------------------

### Get scanner set from hSI.hScan2D

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/ScannerSet%2Band%2BScanners.html

Retrieves the currently configured scanner set from the Scan2D object. The first line gets the read-only set recomputed on configuration changes; the second gets the set used for photostimulation output.

```matlab
ss = hSI.hScan2D.scannerset;         % read-only, recomputed on configuration changes
ss = hSI.hScan2D.stimScannerset;     % the set used for photostimulation output
```

--------------------------------

### hSI.startGrab()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/Acquisition%2BControl.html

Starts a GRAB acquisition: one acquisition of the configured number of frames, volumes, or slices. Logged if `hSI.hChannels.loggingEnable` is set.

```APIDOC
## hSI.startGrab()

### Description
Starts a GRAB acquisition: one acquisition of the configured number of frames, volumes, or slices. Logged if `hSI.hChannels.loggingEnable` is set.

### Method
`startGrab()`

### Parameters
None.

### Returns
None.

### Example
```matlab
hSI.hChannels.loggingEnable = true;
hSI.hScan2D.logFilePath   = 'C:\data';
hSI.hScan2D.logFileStem   = 'experiment_01';
hSI.hScan2D.logFileCounter = 1;

hSI.startGrab();
```
```

--------------------------------

### hSI.hStackManager.setStackStart() / clearStackStart()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/Component%2BAPI/FastZ%2Band%2BStackManager%2BAPI.html

Sets the current z position as the start of a bounded stack, or clears the start position.

```APIDOC
## hSI.hStackManager.setStackStart() / clearStackStart()

### Description
Sets the current z position as the start of a bounded stack, or clears the start position.

### Method
setStackStart() / clearStackStart()

### Parameters
None

### Returns
None
```

--------------------------------

### PowerFunction example

Source: https://docs.scanimage.org/Windows%2BReference%2BGuide/Basic%2BWindows/Power%2BControls/index.html

An example of a custom power function definition in MATLAB, which can be used for Power vs. Depth adjustments.

```matlab
1function powers = myPowerFunction( startPower,zPowerReference,z,lz)
2   powers = sqrt (z-zPowerReference).*startPower;
3end
```

--------------------------------

### Create a RoiGroup and add Rois

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/RoiGroup%2Band%2BRoi%2BAPI.html

Demonstrates initializing an empty RoiGroup, creating Roi objects, adding them to the group, and clearing the group.

```matlab
hRoiGroup = scanimage.mroi.RoiGroup();    % create an empty RoiGroup object

hRoi1 = scanimage.mroi.Roi();             % create an empty Roi
hRoiGroup.add(hRoi1);                     % add hRoi1 to hRoiGroup

hRoi2 = scanimage.mroi.Roi();             % create an empty Roi
hRoiGroup.add(hRoi2);                     % add hRoi2 to hRoiGroup

hRoiGroup.clear();                        % removes all Rois from RoiGroup
```

--------------------------------

### dabs.resources.ResourceStore.showConfig()

Source: https://docs.scanimage.org/Advanced%2BFeatures/ScanImage%2BAPI/dabs%2BAPI/ResourceStore%2BAPI.html

Opens the resource configuration editor.

```APIDOC
## [METHOD] dabs.resources.ResourceStore.showConfig()

### Description
Opens the resource configuration editor.

### Method
showConfig

### Endpoint
`dabs.resources.ResourceStore.showConfig()`

### Parameters
None.

### Request Example
```matlab
dabs.resources.ResourceStore.showConfig();
```

### Response
No return value.
```

--------------------------------

### ScanImage Metadata Dot Syntax Example

Source: https://docs.scanimage.org/Premium%2BFeatures/ALS.html

Example of the dot syntax used for ScanImage parameters when the JSON metadata option is disabled.

```text
SI.hScan2D.sampleRate = 1.2e+08
```
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