# Mosaic3

 Summary: Interfaces with Andor Mosaic 3 Digital Mirror Device (DMD). The Andor Mosaic3 device allows phototargeting of microscope specimens. Author: Arthur Edelstein Documentation: Arthur Edelstein Pariksheet Nanda License: Properietary, closed source, Copyright Andor Technology 2014 Platforms: Windows Devices: MM-820*-SUB MM-820*-SUB-COMP (MM-720* products, i.e. Mosaic I and II devices, are not supported)

## Installation

### Driver

Install the Driver Pack and when prompted for the destination location enter the path where Micro-Manager is installed as shown in the example below.

• Check that the driver for the PCIe card is recognized in the Device Manager as PLDA > PLDA Windows Driver.

### Hardware Configuration Wizard

#### Mosaic

To allow Micro-Manager to control the Mosaic, add the Mosaic3 device using Micro-Manager’s Hardware Configuration Wizard. When you add the device, there are no configuration options.

#### Shutter control of the Projected Light Source

The Mosaic allows a low level of light through even when the digital mirrors are off, and therefore the Mosaic can be optionally purchased with the a physical shutter accessory. This shutter accessory is connected to a Vincent VCM-D1 controller, so to control it in Micro-Manager add the Vincent device.

Shutter control is primarily intended for light sources which cannot be directly modulated, like a Mercury lamp; for light sources that can be modulated, best practice is instead to simply connect the “DMD Active” TTL 5 volt output to your light source “global shutter” (or similar) TTL input so that it is only on when the Mosaic is active. You may not have the shutter accessory installed on if your system was ordered with the intention of using it with this type of TTL light source.

If you have the Power Technology diode laser, you may wish to still add the Vincent device because this laser always leaks ~4mW from the laser head even in the off position (0 volt Analog input). This laser leak is difficult to observe normally since the laser safety interlocks would shut off the laser.

### Calibration

Controlling the Mosaic, like other SLM and Galvo devices, is done by the Projector plugin (Plugins | Device Control | Projector).

Many functions of the generically designed Projector plugin are not useful for the Mosaic. For normal use, one would just open the Projector plugin to go to the ROIs tab and open the Sequencing window.

Before you begin the calibration:

• Make sure a camera has been installed using the Hardware Configuration Wizard.
• In the Setup tab of the Projector plugin:
• If your microscope system requires changing a property for the Mosaic projected light to reach your specimen (often if your imaging reflector cube is different from the mosaic reflector cube), create a Group and a Presets each for your Mosaic reflector and your epi imaging reflector. Assign the Core-ChannelGroup to that Group, and finally in the Phototargeting channel choose the Mosaic reflector preset.
• If you added the Vincent shutter device in the Hardware Configuration Wizard, assign it to the Phototargeting shutter.

You may wish to refer to the Projector Plugin description page if you have not used it before. However, note that for the Mosaic:

• Point and Shoot tab: only projects a fixed-sized round ROI on the live image window and offers no flexibility of shape type and size.
• ROIs tab: is mainly used to open the Sequencing window. The Sequencing window has a super-set of the functionality of the other controls in the ROIs tab.

Focus on a test slide on the microscope stage. The mirror test slide is ideal since it provides a crisp reflection, but if you can’t get a good image from it due to optical filters you can consider a uniform fluorescent slide. Click the Calibrate button. The Projector Plugin will move through a rectangular lattice of spots across the Mosaic array, illuminating them one by one. The corresponding position on the camera image will be automatically measured. During the calibration procedure, a small cross will be visible overlaid on each spot as it is located. When calibration is finished, the plugin will have acquired and stored a coordinate mapping from camera pixels to Mosaic pixels.

## Sequencing window

The Andor Mosaic offers advanced sequencing capabilities. To open the Sequencing Window, in the ROIs tab of the Projector Plugin, click the Sequencing... button. The button also opens the ImageJ ROI Manager.

### ROI list

Use the ROI Manager window to add, remove and update ROIs. If you are not as familiar with ImageJ ROIs or have been using the Mosaic in other software packages, read the Projector plugin’s discussion about drawing multiple ImageJ ROIs.

The intention of the ROI list is to add more properties to each ROI. The list synchronizes itself to contain the same set of ROIs as the ROI Manager.

Column Description
Roi # Reference index number automatically generated. This gets referenced later on in the Sequence table.
Name Copy of ROI name used in ROI Manager.
Mode The default FRAP ROIs appears for short periods of time, whereas Image ROIs are intended to be illuminated throughout the whole sequence.
Intensity Sets the projected light intensity level if you have PixelMode set to one of the gray scale settings.

### Create ROI Grid

To aid a specific use case, this feature duplicates a ROI generating a rectangular grid (lattice) of ROIs. Draw the ROI you wish to duplicate in the upper-left corner of your intended grid, enter the number of ROIs across and down and spacing between lattice points.

### Sequence table

It’s often better to use Create Sequence to populate the sequence table instead of hand-filling an empty Sequence table. The Sequence table is being described first to introduce the nomenclature (particularly the Time Slot) of the Create Sequence generator.

Column Description
Time Slot Reference index number generated by clicking the Generatesequence button in the Create Sequence panel, or by the Add button under under the Sequence table.
ROIs “Roi #” value in ROI list. This can also take a range of Roi #s, e.g. 1-3,5,7,9-11.
On Duration (ms) Illumination time.
Off Duration (ms) Off time after Time Slot
Loops Number of times the ROIs should be repeatedly illuminated within the Time Slot. To repeat the entire Sequence table, set the “Sequence Repeats” number below the Sequence table.

### Create Sequence

ROI sequences consist of a time slots or steps. Within each time slot 1 or more ROIs can be illuminated.

Item

Description

Sequence type

Sequential illiminates each FRAP mode ROI in turn.

Cumulative illuminates the FRAP mode ROI as it progresses through the Time Slots, until all ROIs are illuminated.

Simultaneous mode simply shows all ROIs in a single step.

The remaining items are described in the Sequence table above (On Duration, Off Duration, Loops).

Click the Generatesequence button to populate the Sequence table, below. All Image-type ROIs are included in every step. You can edit the image table to manipulate which ROIs appear in a Time Slot, the On and Off times, and the Loop Count. There are also buttons to Add, Clone, ⌦ Delete, and re-order the Time Slots.

### Control buttons

Below the Sequence table, you can specify:

Item Description
Sequence Repeats Number of many times the Sequence table should be repeated.
Sequence Trigger How the sequence should be triggered.
Upload Sequence Send the sequence and ROIs to the Mosaic device. Get in the habit of clicking this button to apply changes from the Sequence list or from updating ROIs in the ROI Manager.
Run/Stop Execute the sequence. Useful for previewing through the microscope eyepieces or “Live” image on the camera. This button should also be pressed to arm the device for an externally triggered sequence. After clicking this button the device should be prepared to receive an external trigger.
Attach to Acquisition/Detach Executes sequence when running Multi-dimensional acquisition.

## Device Properties

Property

Description

Exposure

Pulse duration of mask in seconds. You would not often change this setting directly since the Sequencing window requires you to set the exposure time in the Sequence list, and the exposure value(s) there takes precedence. Changing this is useful for interactive use e.g. in the Projector > Setup tab.

OverlapMode

Pulses mask when set to Off. Can allow static exposure when set to On.

The Off setting has the benefit of hardware timing accuracy, but it limits the maximum exposure to 200 seconds.

On, by definition, ignores the value of "Off Duration (ms)" in the Sequence window. When combined with setting the Exposure to 0, it exposes the mask constantly; if you have use of this ability one can create, say, an "Exposure Mode" group with a preset named something like "Static".

OperationMode

Choose whether to use hardware or software memory. The default, Live, uses the software memory.

FrameSequence is used with the Sequence window (opening the sequence window automatically changes to this value for you). If you need the SequenceLoopCount to be infinite use ContinuousFrameSequence.

If using FrameIndexSource as Hardware, set to FrameMemory.

FrameIndexSource

Setting this to Hardware allows switching between uploaded Frames using the TTL 26-pin D-sub breakout cable, by setting the "Frame Address [7:0]" BNC inputs. Requires OperationMode being set to FrameMemory.

PixelMode

Switch between BlackAndWhite and several gray scale settings.

GrayScaleExposureTime

Pulse duration of mask in seconds when setting PixelMode to a value other than BlackAndWhite.

InvertMode

Inverts all uploaded masks before projecting. Invert means setting those DMD pixels outside of the 2D ROI On, and those within the 2D ROI Off.

SequenceLoopCount

Number of times to repeat the entire uploaded Frame sequence. You don't need to adjust this since the Sequence window has a textbox for "Sequence Repeats" which takes precedence.

SequenceLoopSettings

Shows result of clicking "Upload Sequence" from Sequence window; useful for debugging. Each "Time Slot" entry from the Sequence window list should appear as
[Time Slot] [On Duration] [Off Duration] [Number of Loops];

TriggerMode

Switch between various internal and external TTL trigger settings which are detailed in the Mosaic manual.

## Scripting

Neither the Projector plugin, nor the Sequencing window, exposes any API. Since they are written in Java, one could edit the Java code itself to add desired functionality. See writing plugins for Micro-Manager

The only scripting possible is that which is already built into MMCore, and thus the “upload bitmap mask” example script detailed below would work on any SLM device. The example script makes use of setSLMImage() and displaySLMImage(), but there are several more SLM functions which one can find by reading through the core documentation and searching for the word “SLM” in the javadoc page.

Create a binary mask from the ImageJ menu by creating a new image (File > New > Image...) and selecting 8-bit Black 800x600. Double-click the dropper tool on the ImageJ toolbar and make sure the current drawing color is white. To draw a freehand shape, double-click the paintbrush tool, set the thickness to, say, 20 pixels and sketch on the image with the paint brush.

Open the Script Panel GUI and paste the following code:

  import ij.IJ; // Allows access to basic ImageJ utilities.
proc = IJ.getImage().getProcessor().duplicate(); // Read the current image.
pixels = proc.getPixels(); // Extract pixels from ImageJ ImageProcessor object.
mosaic = mmc.getSLMDevice(); // Get the installed name of the Mosaic device.
mmc.setSLMImage(mosaic, pixels); // Upload the image to the Mosaic.
mmc.displaySLMImage(mosaic); // Display the Mosaic.


Running this script will result in projecting the image you have just drawn onto the Mosaic.

If you are re-using a saved TIFF image, you need to open it using ImageJ’s File menu (not Micro-Manager’s) and again in the ImageJ menu change Image > Type to 8-bit instead of the default 32-bit (opening as 32-bit is possibly a bug in ImageJ?).

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Discussion page for Mosaic3 imported from old wiki