Manual | Cairn Research
Cairn MultiSplit is designed to provide a simple and intuitive way to process data obtained from a Cairn OptoSplit, TwinCam or MultiCam from within Micro-Manager 2.0.
All files required for running the plugin are contained within the provided JAR file.
Copy this file into the mmplugins subdirectory of your Micro-Manager installation directory.
For example, if Micro-Manager was installed to C:\Program Files\Micro-Manager-2.0 then the file
must be placed in C:\Program Files\Micro-Manager-2.0\mmplugins.
Once installed, the plugin should appear under the Plugins > On-The-Fly Image Processing menu in Micro-Manager.
Note: The file must be placed into the mmplugins directory, not the plugins directory.
| Install Location | |
| On-The-Fly Menu Location | |
| MultiSplit Menu Location | |
To use the software in conjunction with the OptoSplit, configure the camera as normal, snap a reference image and select Plugins > On-The-Fly Image Processing > Cairn MultiSplit. Two windows should open: the "On-The-Fly Processor Pipeline" window and the "Cairn MultiSplit" window.
| Pipeline Setup |  |
| Cairn MultiSplit Window |  |
Next, select the number of channels you want to split the image into using the radio buttons on the right-hand side of the Cairn MultiSplit window.
| Number of Channels Controls |  |
Now draw a rectangular region of interest (ROI) over the reference image corresponding to the location of the first channel and press Select Channel 1. Drag the ROI to the location of the second channel and press Select Channel 2. Repeat this process for as many channels as required.
| ROI Selection |  |
| Select Channel Button |  |
After the second channel is selected, an image window will open displaying the composite image based on your reference and ROIs. At this point you will be able to "nudge" individual channels left, right, up and down using the buttons in the Navigation pane. Pressing the buttons labelled with a single arrow will nudge the specified channel by a single pixel in the corresponding direction, while pressing the buttons labelled with double arrows will nudge the selection by 10 pixels. The channel to be nudged is selected using the radio buttons in the Selection panel, and channels can be hidden by unchecking the corresponding checkboxes.
| Composite Image |  |
| Nudge Channel Selection |  |
Once all regions are selected to your liking, press OK and close the reference image. While the "On-The-Fly Processor Pipeline" window remains open, all new Snaps, live acquisitions and multidimensional acquisitions will automatically be split according to your ROIs.
Pressing the AutoSplit button will automatically draw the appropriate number of channels on your image. For two and three channels the ROIs selected will be vertical splits of equal width; for four channels they will be the top-left, top-right, bottom-left and bottom-right quadrants of the image. This split can either be used as-is or as a starting point for nudging.
To reset the plugin back to its initial state, press the Reset button.
If you accidentally close your reference image, press the Reopen Reference button. This will also redraw the ROI on the image and can therefore be used if you accidentally resize or delete the ROI from the reference image.
Once you have started selecting channels, the Save button will become available. This allows you to save your current ROIs to disk for later use. The Load button can be used to load a previously saved set of ROIs at any time.
Pressing Show Profiles will display the vertical and horizontal line profiles for all channels through each channel's ROI. This display is updated automatically when nudging. Profiles can be disabled by pressing Hide Profiles.
Pressing the Help button will display this manual at any time.
The plugin supports processing of previously acquired data and data acquired outside Micro-Manager with the batch processing options. The Open Reference File button allows the user to open a file from disk to use as a reference instead of snapping an image. The Batch Process button allows the user to select multiple files to split according to the currently entered regions.
To use Cairn MultiSplit with either a TwinCam or MultiCam, first set up the Multi-Camera adapter to use your cameras (instructions on how to do this can be found in the appendix). Snap an image to use as a reference and open the plugin using Plugins > On-The-Fly Image Processing > Cairn MultiSplit. Select the MultiCam tab.
Draw a rectangular ROI over most of the image (making sure to leave enough room for nudging individual channels) and press Select Initial Region. This will open an image window displaying the composite image based on your reference and ROI. At this point you will be able to "nudge" individual channels left, right, up and down using the buttons in the Navigation pane. Pressing the buttons labelled with a single arrow will nudge the specified channel by a single pixel in the corresponding direction, while pressing the buttons labelled with double arrows will nudge the selection by 10 pixels. The channel to be nudged is selected using the radio buttons in the Selection panel, and channels can be hidden by unchecking the corresponding checkboxes.
Once you have finished nudging the channels to their desired positions, press the OK button and close the reference image. While the "On-The-Fly Processor Pipeline" window remains open, all new Snaps, live acquisitions and multidimensional acquisitions will automatically be split according to your ROIs.
To reset the plugin back to its initial state, press the Reset button.
If you accidentally close your reference image, press the Reopen Reference button. This will also redraw the ROI on the image and can therefore be used if you accidentally resize or delete the ROI from the reference image.
Once you have started selecting channels, the Save button will become available. This allows you to save your current ROIs to disk for later use. The Load button can be used to load a previously saved set of ROIs at any time.
Pressing Show Profiles will display the vertical and horizontal line profiles for all channels through each channel's ROI. This display is updated automatically when nudging. Profiles can be disabled by pressing Hide Profiles.
Pressing the Help button will display this manual at any time.
The plugin supports processing of previously acquired data and data acquired outside Micro-Manager with the batch processing options. The Open Reference File button allows the user to open a file from disk to use as a reference instead of snapping an image. The Batch Process button allows the user to select multiple files to split according to the currently entered regions.
The Sequential mode is designed for use with the Cairn OptoSpin and MultiStreams. To enable sequential mode, navigate to the Sequential tab and select the Enable checkbox. The channel associated with each image can then be selected from the drop-down menus. Images may also be assigned Skip, in which case they will be ignored.
Note: Only one channel may be assigned to each image slot.
| Sequential Mode |  |
The following tables show example configurations for different filter wheel setups.
| Filter Position | Filter at Position | Sequential Mode Settings |
|---|---|---|
| 1 | Red | Image 1: Channel 1 |
| 2 | Green | Image 2: Channel 2 |
| 3 | Blue | Image 3: Channel 3 |
| 4 | Red | Image 4: None |
| 5 | Green | Image 5: None |
| 6 | Blue | Image 6: None |
| Filter Position | Filter at Position | Sequential Mode Settings |
|---|---|---|
| 1 | Red | Image 1: Channel 1 |
| 2 | Green | Image 2: Channel 2 |
| 3 | Blue | Image 3: Channel 3 |
| 4 | None | Image 4: Skip |
| 5 | None | Image 5: Skip |
| 6 | None | Image 6: Skip |
| Filter Position | Filter at Position | Sequential Mode Settings |
|---|---|---|
| 1 | Yellow | Image 1: Channel 4 |
| 2 | Blue | Image 2: Channel 3 |
| 3 | Green | Image 3: Channel 2 |
| 4 | Red | Image 4: Channel 1 |
| 5 | None | Image 5: Skip |
| 6 | None | Image 6: Skip |
| Filter Position | Filter at Position | Sequential Mode Settings |
|---|---|---|
| 1 | Red | Image 1: Channel 1 |
| 2 | None | Image 2: Channel 2 |
| 3 | None | Image 3: None |
| 4 | Green | Image 4: None |
| 5 | None | Image 5: None |
| 6 | None | Image 6: None |
To reset the plugin back to its initial state, press the Reset button.
Pressing the Help button will display this manual at any time.
The plugin supports processing of previously acquired data and data acquired outside Micro-Manager with the batch processing options. The Batch Process button allows the user to select multiple files to process, according to the current sequential mapping.
This plugin uses JFreeChart, Copyright
JFree.org and Contributors, licensed under the
GNU Lesser General Public License (LGPL) version 2.1.
A copy of the license is included in this plugin's jar file under
META-INF/licenses/JFREECHART-LGPL-2.1.txt.
A relinking script (relink-jfreechart.gradle.kts) is available from Cairn
Research to rebuild this plugin with a different version of JFreeChart, as
permitted by the LGPL.
Support for running multiple cameras in Micro-Manager is given by the Multi-Camera device adapter.
Once the hardware configuration is finished, you may get the error message "Failed to initialize circular buffer — memory requirements not adequate". This is due to the Multi-Camera adapter not currently knowing how large a single frame will be and can be ignored at this point.
Open the Device Property Browser and set Multi Camera — Physical Camera 1–4 to your camera names (or "Undefined" if you do not want to use all four camera slots). Set up your camera properties and close the Device Property Browser. Clicking Snap should now show a single image with multiple channels — one channel per camera.