Prerequisites cont’d

For technicians and sales managers!

Since the software version 1.14 usable scan cameras as well as other settings of the scanner are defined in the dialogue “Microscope settings” in the menu “Options” of the selector dialogue.

Adimec Q-12A180 CXP

Grasshopper 3

VCC-F52U25CL

VCC-FC60FR19CL

PCO.edge 5.5Mp CL

PCO.edge 4.2Mp CL

AxioCam MRm Rev.3

Stingray F-146C IRF MEDICAL

Marlin F-146C IRF MEDICAL

Hitachi HV-F22CL

Sony DFW-X710

All cameras with “CL” (Camera Link interface) in the name will be handled via the SOLIOS or the RADIENT board!

“Base Settings”

All hardware (camera implementation or exchange) and driver modifications have to be done prior to starting the program SlideScanner.exe and the dialogue “Base Settings”; the driver have to be already installed, the camera have to be connected and powered on!

The objective settings should be done or checked together with the setup of the camera(s); the items (1) to (4).

“Setup and define implemented objectives”

Pos. 1: Camera type (FL-camera)

By opening the pull down menu (5) one of the implemented cameras can be selected. The selected camera type has to be identical with the connected camera type.

If the Pannoramic scanner is equipped with a camera changer unit, the fluorescent scan camera has to be defined here.

If the 90º camera tube is installed, the brightfield camera has to be defined here.

“Camera positions on the camera changer”.

“90º camera tube”.

Check this checkbox (6), (9) if the selected camera should be used for brightfield scan.

Check this checkbox (6), (9) if the selected camera should be used for fluorescent scan.

Check both checkboxes if the camera should be used for BF and FL scan operation (if only one camera is installed or for test purposes).

Adapter magnification

Select the real value for the camera adapter magnification (7), (10); it can be found on the camera adapter itself.

Pos. 2: Camera type (Brightfield camera)

If the Pannoramic scanner is equipped with a camera changer unit the brightfield camera has to be defined here. The camera, defined for position 1 will be excluded from the list of this pull down menu. Furthermore, if the position 1 camera was defined as FL scan, the position 2 camera can be defined for BF scan only and vice versa (8).

“Camera positions on the camera changer”.

“90º camera tube”.

Test and Apply Camera Settings

The defined camera type(s) will be checked for system integrity (11). If the result of the check is positive, the camera types are accepted and are integrated into the system; the success is shown with a “” mark beside the selected camera type. An information window shows the result of the check.

If there is trouble with any selected camera an error message occurs; the unsuccessful integrity is shown with a “” mark.

Success of camera integrity check

Camera integrity check failed

If the camera integrity check has failed

Check the Camera Link connection between Solios board and camera; the cables should be connected to the appropriate port (connector) and the lock bolts should be tightened on all four headers.

· Check the power of the camera; the power connector should be connected well; the camera should be switched on.

· Check the enable or disable state of the “Power distribution and switch board” in the file “MicroscopeConfiguration.ini” or check the external power supply (if present).

Check the correct power connector position on the “Power distribution and switch board”.

· Check the trigger cable and its connection between camera and “X-Y-Z-ND motor & flash light control” electronics; the trigger connector should be connected right.

· See also: “Camera CIS-VCC-F52U25CL” and “Camera pco.edge” respectively

Check the port (cable connection and power supply) of the failed camera, the installation of the MIL_9.0 or the driver installation.

Important

If the switch “TRG” or “Vref” of the flash light source is not set to “External” the camera installation may be not finished correctly in the dialog “Microscope settings” or the scan program fails the camera installation with the error message.

Sensor characteristics

Following tables summarizing parameters of the preview and scan cameras in optical aspects for scanning purposes.

Preview cameras
Camera	Effective pixel array size		Active pixel size
Camera	(H) pixels	(V) pixels	(H) µm	(V) µm
VRmagic	2056	1544	3.2	3.2
Used:	2048	1536	3.2	3.2
DFK 21F04	640	480	5.6	5.6

Preview camera pixel view = (Preview camera pixel size) * (Preview objective magnification)

Preview objective magnification DFK 21F04 ~ 8.2x

Preview objective magnification VRmagic ~ 4.7x

· Preview camera pixel view DFK 21F04 = 46µm

· Preview camera pixel view VRmagic = 15µm

Useable magnifications and resulting resolutions of scan (main) cameras
Camera	Pixel array size used ; [Pixels]		Pixel size [µm]			Useable Magnification; Resolution [µm]
	Pixel array size used ; [Pixels]		Active		Valid	0.63x		1.0x		1.6x
	(H)	(V)	(H)	(V)	(H or V)	20x	40x	20x	40x	20x	40x
Grasshopper3; color* ³⁾	2448	2048	3.45	3.45	4.87*	0.39	0.19	0,24	0.12	X	X
Stingray*	1380	1030	4.65	4.65	6.58*	0.52	0.26	0.33	0.16	X	X
Marlin* ¹⁾	1368	1024	4.65	4.65	6.58*	0.52	0.26	0.33	0.16	X	X
Adimec Q-12A180* ²⁾	4096	3072	5.5	5.5	7.78*	X	X	X	X	0.24	0.12
CIS-VCC F52U25CL	1624	1224	4.40	4.40	4.40	0.35	0.18	0.22	0.11	X	X
CIS-VCC FC60FR19CL*	2048	2048	5.5	5.5	7.78*	X	X	0.39	0.19	0.24	0.12
Hitachi HV-F22CL	1360	1024	4.65	4.65	4.65	0.37	0.18	0.23	0.12	X	X
Sony DFW-X710* ¹⁾	1024	768	4.65	4.65	6.58*	0.52	0.26	0.33	0.16	X	X
Monochrome scan cameras (FL or RGB illuminated)
Grasshopper3; mono³⁾	2448	2048	3.45	3.45	3.45	0.27	0.14	0,17	0.08	X	X
AxioCam MRm R3	1388	1040	6.45	6.45	6.45	X	X	0.32	0.16	X	X
PCO-edge 4.2	2048	2048	6.5	6.5	6.5	X	X	0.32	0.16	X	X
PCO-edge 5.5_@ 2.5Mp	1600	1600	6.5	6.5	6.5	X	X	0.32	0.16	X	X
PCO-edge 5.5_@ 4.0Mp	1920	1920	6.5	6.5	6.5	X	X	0.32	0.16	X	X
PCO-edge 5.5_PCON	2560	2160	6.5	6.5	6.5	X	X	0.32	0.16	X	X

X) Not defined, can not be used

* Calculations for these cameras are done by using the factor sqrt(2)

Resolution [µm] = (Active camera pixel size * sqrt(2) ) / (objective magnification * camera adapter magnification); used if single chip camera with Bayer method

· sqrt(2)= required, because debayering (creation of color information in single chip cameras with Bayer method); and generation of JPEG file

If real color camera or monochrome (FL) camera:

Resolution [µm] = (Active camera pixel size) / (objective magnification * camera adapter magnification)

1) No longer delivered

2) Useable since SW version 1.20 only!

3) Useable since SW version 1.21only!

Adimec Q-12A180

Used in: P250 FLASH 3, SW-version 1.20 and higher

The Adimec QUARTZ Q-12A180 is a12 Megapixel camera at 187 fps with a maximum of only 9W power consumption in a small outline; with the highest image quality today and the QUAD CoaXPress interface.

Sensor

· Type: CMV12000

· Global shutter CMOS

· A/D conversion 32 channels 8 or 10bit ADC

· Optical size APS-C

· Resolution 12MPixels - 4096(H) x 3072(V)

· Pixel size 5.5 x 5.5 μm

· Active pixels 4096 (H) x 3072 (V)

· Frame rate 300 fps (10 bit)

132 fps (12 bit)

· Chroma Mono, Mono NIR enhanced and RGB

Triggering Internal or external

Power Input 24Vdc PoCXP (Power over CXP)

Operating temperature -10°C to +30°C

Interface CoaXPress; Configurable 1, 2 or 4 lanes

Board: Matrox Radient eV-CXP; PCIe 2.0 x8, PoCXP

”Specifications” (stored); “CoaXPress”; “Multyway-connector” (stored); “Matrox_Radient_ev_cxp.pdf” (stored)

If the LED of any wire is flashing red, then the appropriate line is not recognized or not connected or the line is not controlled yet by software!

Power

The power for the camera is provided over the CXP cables

Important

To provide power for the camera the internal power connector of the Radient eV-CXP board has to be connected with the power supply!

Cabling

See the images on the right

If the LED of any wire is flashing red, then the appropriate line is not recognized or not connected or the line is not controlled yet by software!

Trigger

Camera adapter

Because the camera Adimedc has a very large CMOS sensor, the camera is always used with a camera adapter of 1.6x

Camera Grasshopper 3

Manufacturer: POINTGREY

Model: GS3-U3-51S5 M-C; monochrome and

GS3-U3-51S5 C-C; Color

Monochrome version used in: delivered S_M_D type scanners since summer 2016 as BF and FL scan camera or in other scanner types as FL scan camera

Color version used in: scanner types, delivered before summer 2016, as BF scan camera

SW Version: 1.21 or higher.

Interface type: USB 3.0

Power: Supplied over USB 3.0 or external; 4.5W max.

The Grasshopper3 is an USB 3.0 interfaced monochrome scan camera, used mainly in improved SCAN, MIDI and DESK type scanners delivered since summer 2016, as BF and FL scan camera. In systems with camera changer unit the camera may be used as FL scan camera.

The camera requires the software version 1.21. Because improved S_M_D type scanners got an RGB brightfield scan illumination unit, the FOV is captured three times, one time by each color. The 3 gray scale images, taken by the Grasshopper3 monochrome camera, define the partial intensity of the appropriate color. By assembling the raw RGB images and using the software coloring method, images of a very high quality and color fidelity with improved resolution can be produced.

The color version of the camera may be used in upgraded Pannoramic type scanners with Halogen lamp BF illumination; it offers higher pixel resolution and higher image transfer speed.

Improvements

· Only one camera is required for BF and FL scan sessions

· Camera changer unit not required

· Higher scan quality, faster scan speed

· Higher pixel resolution

· 10 times faster image transfer over USB3.0 (in relation to Stingray camera)

Features; GS3-U3-51S5
Parameter	M-C (mono)		C-C (color)
Resolution (H x V)		2448 x 2048	2448 x 2048
Pixel Size		3.45 µm	3.45 µm
Megapixels		5.0 MP	5.0 MP
Chroma		Mono	Color
Sensor Name		Sony IMX250	Sony IMX250
Sensor Type		CMOS	CMOS
Readout Method		Global shutter	Global shutter
Sensor Format		2/3"	2/3"
Frame Rate		75 FPS	75 FPS
Lens Mount		C-mount	C-mount
ADC		10-bit and 12-bit	10-bit and 12-bit
Interface		USB 3.0	USB 3.0

POINTGREY home page

Getting started manual (stored)

Technical Reference (stored)

Imaging Performance (stored)

Data sheet (stored)

Important

Please use always a FRESCO FL 1100 USB 3.0 interface board, type U3-PCIE1XG211 to interfacing Grasshopper3 type cameras in Pannoramic Scanners.

· By using other USB 3.0 interface ports, the camera might not work.

Interface board USB3.0

Trigger

HW triggering

If an RGB brightfield illumination unit is used and the camera works as BF scan camera (S_M_D), the camera will be triggered by the trigger output of the scanner.

Two types of trigger cable are used:

LTF-2: The scanner’s USB control electronics triggers the camera

LTF-3: The scanner’s USB control electronics triggers the camera and the lumencor spectra light engine©

SW triggering

If the camera works as FL scan camera in scanners with camera changer, the camera will be triggered by software.

Getting started manual (stored)

Driver setup

Camera CIS- VCC-F52U25CL

Used in: P250, SCAN, MIDI and DESK

The VCC-F52U25CL is a camera link interfaced, 3CCD high-resolution industrial color video camera module utilizing a 1/1.8 type PS IT CCD. The 2M pixels CCD image sensor with on-chip micro-lenses realizes high sensitivity and high resolution. The full size field of view can be read out within approx. 30fps.

CIS- VCC-F52U25CL

Device Type: 1/1.8 type Interline Transfer Color CCD

CCD: SONY ICX274AL

Effective Pixel Number: 1628 (H) × 1236 (V)

Unit Cell Size: 4.40μm (H) × 4.40μm (V)

Chip Size: 8.50mm (H) × 6.80mm (V)

“Possible scan modes with different cameras and magnifications in the software version 1.16; 1.17beta and 1.17

“Useable magnification and resulting resolution for scan (main) cameras”

Further information about features, precautions and detailed technical information can be found in the file “vcc-f52u25cl_en.pdf”.

Power

The camera gets its power of 12V-DC, 6.0W by default from the “Power distribution and switch board” of the scanner.

The camera interface is a so called “Hot plug interface” so the cable header may be removed or plugged during the computer is powered on, but wait until the data transfer between camera and link board is finished (if in progress).

Nevertheless, the camera should be powered off before any connection modification is taken.

Unplug the power header of the camera or switch off the entire scanner.

Make the desired connections and secure the header connection with the lock bolts.

Switch on the scanner, or plug the power header.

Check the camera integrity or implementation with the dialogue “Microscope Settings”.

Triggering

The trigger input pulse width of the camera as well as the width of the trigger pulse of the flash light source is controlled by the firmware. The trigger cable of the camera is connected to the appropriate connector of the “X-Y-Z-ND motor and flash light control” electronics.

External power supply

This power supply is used if the CIS-camera works in SCAN or MIDI scanners.

The timing of the camera’s shutter in the SCAN or the MIDI is realized by software.

Camera Link connection

Both camera link cables are from the same type and the headers are wired 1:1, so any cable header can be connected to the Solios board or to the camera as well.

Important

The Camera link cable, connected to the port “CL1” of the camera have to be connected to the “Channel 0” of the Solios board; and the Camera link cable, connected to the port “CL2” of the camera have to be connected to the “Channel 1” of the Solios board.

If these conditions are not met, the camera will not be found or recognized by the software!

“Solios board SOL2MEVCLF*”

“Matrox RADIENT eCL board”

Important

Driver install

The CIS-camera is fully handled by the scan software “SlideScanner.exe” via the Solios board; therefore, an explicit driver installation procedure is not required.

“Setup the Matrox Imaging Library version 9.0 (MIL 9.0)”

Camera CIS VCC-FC60FR19CL

Used in: iSaCS, P250, SCAN, MIDI and DESK

The VCC-FC60FR19CL is a camera link interfaced, 4Mpixels high-resolution industrial color video camera module. The 4M pixels global shutter CMOS sensor realizes high sensitivity and high resolution. The full size field of view can be read out within 135fps, depending on the configuration.

VCC-FC60FR19CL

Device type: Color CMOS

Diagonal length: 15.930mm

Shutter type: Global

Effective pixel number: 2048 (H) x 2048 (V)

Cell size: 5.5μm (H) x 5.5μm (V)

Frame rate: 68 to 135fps; depending on configuration

“Possible scan modes with different cameras and magnifications in the software version 1.16; 1.17beta and 1.17

“Useable magnification and resulting resolution for scan (main) cameras”

Further information about features, precautions and detailed technical information can be found in the Product Specification and Operational Manual “Spec_VCC-FC60FR19CL.pdf ”.

The switch

CL: In this position the power is supplied via the “Power & trigger” connector (DC IN).

PoCL: The power is supplied via the camera link interface (PoCL= Power over Camera Link).

Set the switch into the position “CL” and use the power and trigger connector!

Remove the CMOS sensor protector and mount the conversion ring.

Power; P250

The camera gets its power of 12V-DC, 3.0W by default from the “Power distribution and switch board” of the scanner.

The camera interface is a so called “Hot plug interface” so the cable header may be removed or plugged during the computer is powered on.

Nevertheless, the camera should be powered off before any connection modification is taken.

Unplug the power header of the camera or switch off the entire scanner.

Make the desired connections and secure the header connection with the lock bolts.

Switch on the scanner, or plug the power header.

Check the camera migration with the dialogue “Microscope Settings”.

Power; S_M_D

Please refer to “External power supply”

Triggering

Camera Link connection

Both camera link cables are from the same type and the headers are wired 1:1, so any cable header can be connected to the grabber card RADIENT eCL (or to the Solios board, if only 1 camera is used in the scanner) or to the camera as well.

Important

The Camera link cable, connected to the port “CL1” of the camera have to be connected to the “Channel 0” of the grabber card RADIENT eCL; and the Camera link cable, connected to the port “CL2” of the camera have to be connected to the “Channel 1” of the grabber card RADIENT eCL.

If these conditions are not met, the camera will not be found or recognized by the software!

“Solios board SOL2MEVCLF*”

“Matrox RADIENT eCL board”

Important

Driver install

The camera CIS is fully handled by the scan software “SlideScanner.exe” via the RADIENT eCL board; therefore, an explicit driver installation procedure is not required.

“Setup the Matrox Imaging Library version 9.0 (MIL 9.0) Radient eCL”

Camera PCO-edge 5.5MP

Used in: PCON, P250, SCAN and MIDI

The pco.edge is a camera link interfaced, monochrome camera and is used for scanning of stained tissues in the fluorescent scan mode. In the scanner type “PCON” all scan modes are handled with this camera. The color (wave length of the light) is defined by the used filter block and the gray scale image, taken by the pco.edge camera, defines the partial intensity. By using the software coloring method, images of a very high quality and color fidelity can be produced.

PCO.edge

Sensor: Scientific CMOS

Resolution: 5.5Mpixels

Pixel array: 2560 (H) x 2160 (V)

Pixel size (h x v): 6.5 µm x 6.5 µm

Transfer rate: 100fps (full size)

Power requirements

Input: 12 … 24 VDC (+/- 10 %)

Power consumption: 20W max. (typ. 10 W @ 20°C)

Remark

This camera is used in some configurations with a smaller sensor size, the size is reduced by software.

In these cases, the camera is named as

· PCO-edge_5.5_@2.5MP and

· PCO.edge_5.5_@_4.0MP

More information about sensor size and resolutions can be found on the shown links.

“Possible scan modes with different cameras and magnifications in the software version 1.16; 1.17beta and 1.17

“Useable magnification and resulting resolution for scan (main) cameras”

Information about features, precautions and others can be found in the file: “pco_edge_20110527.pdf”

or further, detailed technical information: “pco_edge_manual_V1-01.pdf” (stored).

Camera Link connection

The data transfer between camera and Solios board is realized with two Camera link cables.

Both camera link cables are from the same type and the headers are wired 1:1.

The cable header on the Solios board side is a “Camera link HDR26” (CL mini) type connector during on the camera side a “Camera link (CL) original” type cable header is used.

Important

The Camera link cable, connected to the port “CameraLink A” of the camera have to be connected to the “Channel 0” of the Solios board; and the Camera link cable, connected to the port “CameraLink B” of the camera have to be connected to the “Channel 1” of the Solios board.

If these conditions are not met, the camera will not be found or recognized by the software!

“Solios board SOL2MEVCLF*”

“Matrox RADIENT eCL board”

Driver install

The camera PCO.edge is fully handled by the scan software “SlideScanner.exe” via the Solios board(s); therefore, an explicit driver installation procedure is not required.

Power; P250

The camera gets its power of 12V- DC 15W by default from the “Power distribution and switch board” of the scanner; in exceptions or special conditions an external power supply may be used (e.g. SCAN, MIDI).

Nevertheless, the camera should be powered off before any connection modifications are done.

Switch of the camera or unplug the power header or switch off the entire scanner.

Make the desired connections and secure the header connection with the lock bolts.

Switch on the scanner, the camera or plug the power header.

Triggering

The trigger output 4 of the camera is used to trigger the Lumencor SPECTRA light engine.

In SCAN_II and MIDI_II type scanners the trigger cable LTO-4 is used.

External power supply

This power supply is used if the PCO.edge camera works in SCAN or MIDI type scanners.

PCON

The principle of triggering is the same as for the P250 but cable headers are modified!

The trigger output 4 of the camera is used to trigger the Lumencor SPECTRA light engine and the RGB illumination unit.

Control, cables and connections

Camera PCO-edge 4.2Mp

Used in: P250, SCAN, MIDI

The pco.edge 2.4M is a camera link interfaced, monochrome camera and is used for scanning of stained tissues in the fluorescent scan mode. The color (wave length of the light) is defined by the used filter block, the wavelength of the exciting light beam and the gray scale image, taken by the pco.edge camera defines the partial intensity. By using the software coloring method, images of a very high quality and color fidelity can be produced.

PCO.edge

Sensor: Scientific CMOS

Resolution: 4.2Mpixels

Pixel array: 2048 (H) x 2048 (V)

Pixel size (h x v): 6.5 µm x 6.5 µm

Transfer rate: 100fps (full size)

Power requirements

Input: 12 … 24 VDC (+/- 10 %)

Power consumption: 20W max. (typ. 10 W @ 20°C)

“Possible scan modes with different cameras and magnifications in the software version 1.16; 1.17beta and 1.17

“Useable magnification and resulting resolution for scan (main) cameras”

Information about features, precautions and others can be found in the file: “BR_pco_edge42_105_online.pdf”

or further, detailed technical information: “pco_edge_manual_V1-01.pdf”.

Camera Link connection

The data transfer between camera and Solios board is realized with two Camera link cables.

Both camera link cables are from the same type and the headers are wired 1:1.

The cable header on the Solios board side is a “Camera link HDR26” (CL mini) type connector during on the camera side a “Camera link (CL) original” type cable header is used.

Important

If these conditions are not met, the camera will not be found or recognized by the software!

“Solios board SOL2MEVCLF*”

“Matrox RADIENT eCL board”

Power; P250

Nevertheless, the camera should be powered off before any connection modifications are done.

Switch of the camera or unplug the power header or switch off the entire scanner.

Make the desired connections and secure the header connection with the lock bolts.

Switch on the scanner, the camera or plug the power header.

Power; SCAN and MIDI

External power supply

Triggering

The trigger output 4 of the camera is used to trigger the Lumencor SPECTRA light engine.

Driver install

The camera PCO.edge 4.2Mp is fully handled by the scan software “SlideScanner.exe” via the Solios board(s); therefore, an explicit driver installation procedure is not required.

“Setup the Matrox Imaging Library version 9.0 (MIL 9.0)” and “Solios board”

Camera AxioCam MRm REV.3

Used in: P250, SCAN and MIDI

The AxioCam MRm Rev.3 camera is a 12 bit monochrome camera especially used for fluorescent scan. The color (wave length of the light) is defined by the used fluorescent filter and the gray scale image, taken by the AxioCam camera defines the intensity. By using the software coloring method, images of a very high quality and color fidelity can be produced.

CARL ZEISS Monochrome camera for fluorescent scan

Video Data output: 12 bit

Frame rate: MAX. 13 FPS

Effective pixels: 1388 x 1040 (1.4 Mega pixels)

Cell size: 6.45 x 6.45 μm

Pixel resolution (with 20x objective and C-mount adapter 1x): 0.33μm

Interface type: IEEE 1394a

More information about features, precautions and others can be found in the file “AxioCam MRm Rev.3”

“Useable magnification and resulting resolution for scan (main) cameras”

Requirements

FireWire IEEE 1394 “a” header type controller (card)

FireWire IEEE 1394 “a” to “a” header type cable

Install and driver CD for Pannoramic scanners, “AxioCam.inf”

Cables and connections

The camera cable connection is realized with an IEEE 1394 “a” type header and the cable is connected to the inserted controller board with a FireWire IEEE 1394 “a” type or “b” screw lock type header. The camera needs a FireWire port of the extension card. The camera has a FireWire input port (connected to the computer) and a link port (connected to the next camera; not used in Pannoramic scanners). If the camera is not recognized after driver installing, please try with the other port connector of the camera.

“FireWire interface”, “Precautions” and “Connect the camera”

Driver install

· Windows® 7x64bit Setup the driver for the camera “Carl Zeiss AxioCam MRm R3”

· Windows® XP Setup the XP driver for the camera “Carl Zeiss AxioCam MRm R3”

Stingray F-146C IRF MEDICAL

Used in: SCAN, MIDI and DESK

The camera uses a single chip CCD and produces pictures of a good quality, and is used for brightfield and fluorescent scan likewise. Because the sensitivity of this camera is very high and the RGB logic contains a hardware equalizer, the color fidelity is also high.

Further information about “Single chip CCD color capturing” and

‘Single chip CCD” Wikipedia

AVT Stingray color camera Fire Wire 1/2" type progressive SCAN IT CCD

Video data output: 8/14 bit

Frame rate: ~15 FPS

Effective pixels: 1388 x 1038 (1.44 Megapixels)

Cell size: 4.65 x 4.65μm

Pixel resolution (with 20x objective and C-mount adapter 1x): 0.23 μm

Interface type: IEEE 1394b, screw lock

“Useable magnification and resulting resolution for scan (main) cameras”

“Stingray_DataSheet_F-146_V4.0.1_en.pdf”, “”

Requirements

Fire wire IEEE 1394 “b” screw lock type controller board

Fire wire IEEE 1394 “b” screw lock type cable

Install and driver CD for Pannoramic scanners AVT Fire package

Cables and connections

The camera cable connection is realized with an IEEE 1394 “b” screw lock type header and the cable is connected to the inserted controller board with a FireWire IEEE 1394 “a” type or “b” screw lock type header. The camera needs a FireWire port of the extension card. Because the AVT fire package uses the entire controller of the board, no other type cameras (like the DFK21F04) can be connected to this controller (card). The camera has a FireWire input port (connected to the computer) and a link port (connected to the next camera; not used in Pannoramic scanners). If the camera is not recognized after driver installing, please try with the other port connector of the camera also.

“FireWire interface”, “Precautions” and “Connect the camera”

Check or set the following entries of the file “MicroscopeConfiguration.ini” (until SW version 1.14):

[Microscope]

ScanCameraType= AVT Stingray F146C

[ScanCamera]; the following parameter values are for information only!

Gain=0

Shutter=1000

Gamma=0

Saturation=128

Hue=128

WhiteBalance_U=81

WhiteBalance_V=45

Sharpness=0

Brightness=0

TriggerTimeout=5000

AutoCalibrate=TRUE

Check / set the following entries of the file “MicroscopeSettings.ini”:

[ReflectorTurret]

CameraName = Stingray F146C

Driver install

· Since the software version 1.16 Setup_AVT_cam_Driver Windows® 7x64bit

· Until the software version 1.14 Setup AVT_XP_FirePackage Windows® XP x 32bit

Marlin F-146C IRF MEDICAL

Used in: SCAN, MIDI and DESK

The camera uses a single chip CCD and produces color pictures of a good quality; it is used for brightfield and fluorescent scan likewise. Because the sensitivity of this camera is very high and the RGB logic does not contain a hardware equalizer, the illumination of the FOV must be adjusted very well, otherwise the color fidelity is reduced. This is the reason why in newer systems this camera is replaced by the camera “Stingray F-146C IRF MEDICAL”.

Resolution: 1392 x 1040

Data rate: 400 Mbit/s max.

Speed: 17 fps max.

Interface type: IEEE 1394a

“Useable magnification and resulting resolution for scan (main) cameras”

“Marlin_DataSheet_F-146_V4.0.0_en.pdf”” and ”Sngle chip CCD color capturing”

Requirements

Fire wire IEEE 1394 “a” type controller card

Fire wire IEEE 1394 “a” type cable

Install and driver CD for Pannoramic scanners; AVT Fire package

Cables and connections

The camera is connected to the inserted controller board with a FireWire IEEE 1394 “a” type cable. The camera needs a FireWire port of the extension card. Because the AVT fire package uses the entire controller of the board, no other type cameras (like the DFK 21F04) can be connected to this controller.

“FireWire interface”, “Precautions” and “Connect the camera”

Driver install

· Since the software version 1.16 Setup_AVT_cam_Driver Windows® 7x64bit

· Until the software version 1.14 Setup AVT_XP_FirePackage Windows® XP x 32bit

HITACHI HV-F22CL

Used in: SCAN, MIDI and DESK

The camera contains for the colors red green and blue a separate CCD; it is a “Three CCD camera”. Each CCD uses a 10 bit A/D converter so the color fidelity is very high. Because the camera uses an own interface board and own interface cables (Data-Link interface), the transfer rate is very high as well. Primarily the camera is advised for brightfield scan procedures but there can be produced fluorescent scans with a high quality as well.

Hitachi HV-F22CL 3CCD progressive scan color camera

Video Data output: 3 x 10 bit

Frame rate: ~15 FPS

Effective pixels: 1360 x 1024 (1.4 Megapixels)

Cell size: 4.65 x 4.65μm

Pixel resolution (with 20x objective and C-mount adapter 1x): 0.23 μm

“Useable magnification and resulting resolution for scan (main) cameras”

“HV-F22CL Specifications”, “Operation_Manual”, Technical_information”

Requirements

The Matrox Solios XCL controller board; delivered with the camera

Interface cables; delivered with the camera

Power supply; delivered with the camera

Matrox Imaging Library MIL 8.0 or MIL 9.0; to install the hardware

“Solios board SOL2MEVCLF*”

“Matrox RADIENT eCL board”

Cables and connections

The Matrox Solios XCL controller board should be inserted into a PCI slot with 64bit /66MHz or higher (in software versions until 1.14)!. The camera is connected to the computer with the D.OUT1 and D.OUT2 data link cables to the appropriate connectors of the Solios board. The delivered power supply is connected to the DCIN / SYNC input of the camera.

The installation of the board and the driver installation procedures are suggested to be done by a qualified system administrator.

Important

The Solios board should be inserted into a slot PCI-E generation 1 (PCI-Express x8 gen.1); otherwise, if a PCI-E generation 2 slot is used, the system may freeze during boot (in software versions until 1.14)!

Detailed information about hardware install and software setup procedures can be found on the Install CD for Pannoramic scanners in the files:

<CD ROM>:Drivers\Matrox Imaging Library\ Matrox Imaging Library Installation Guide MIL 8.0 or MIL9.0 respectively

And

<CD ROM>:Drivers\Matrox Imaging Library\Hitachi HV-F22CL (Original CD)\Doc\ English \Operation_Manual

Check or set the following entries of the file “MicroscopeConfiguration.ini” (until SW version 1.14):

[Microscope]

ScanCameraType=Hitachi_HV_F22CL

[ScanCamera]; until SW version 1.14; the following parameter values are for information only!

Gain=0

Shutter=1000

Gamma=0

Saturation=128

Hue=128

WhiteBalance_U=86

WhiteBalance_V=44

Sharpness=0

Brightness=0

TriggerTimeout=5000

AutoCalibrate=TRUE

Check or set the following entries of the file “MicroscopeSettings.ini”:

[ReflectorTurret]

CameraName = Hitachi_HV_F22CL

To install the camera driver for the camera Hitachi HV-F22CL

Please refer to the file:

<CD ROM>\Drivers\Matrox Imaging Library\ Matrox Imaging Library Installation Guide.doc

Sony DFW-X710

Used in: MIRAX SCAN and MIRAX DESK

The Sony camera uses a single chip CCD and was used in early SCAN, MIDI and DESK scanner systems until the spring of the year 2007; the production of the camera was discontinued. The camera produces pictures of a good quality, and is used for brightfield and fluorescent scan likewise. Today, this camera is no longer delivered but earlier developed systems may use this camera further (in Windows © XP surrounding).

Progressive scan CCD

Frame rate: 15 fps max.

Resolution: 1024 x 768

Cell size: 4.65 x 4.65μm

Transfer speed: 400/200 Mbps (400 with external triggering)

Interface type: IEEE 1394a

“Useable magnification and resulting resolution for scan (main) cameras”

Manuals: DFW_SX910_X710_s, dfw-sx910-x710_data

Further information can be found in the chapter “Sony_DFW_X710_cam_and_driver”

Lumencor SPECTRA light engine®

The Lumencor SPECTRA Light Engine® is a light source, used to illuminate the field of view of fluorescent stained tissues; the required light wavelengths are created by light modules. The light modules are switched on or off separately, as required for the excitation wavelength to be used.

· The Lumencor SPECTRA Light Engine® is delivered together with the PCO.edge FL scan camera.

· The following chapter is true for the PSCAN and the PMIDI also.

Features

· The use of a separate light module for each excitation wavelength allows the precise creation of the required light wavelength.

· The light sources are switched separately and electronically, software controlled.

· The exchange of the excitation wavelength is done very quickly.

· The use of multiple band filters is possible.

· Minimizing of mechanical movements (of the filter wheel) saves scan time.

· Bleaching of the fluorescent tissue is minimized, because the exciting light is switched on only during the shutter time of the camera (hardware triggering).

· Low heat emission.

· Low power consumption.

· The scan process of the virtual tissue in the fluorescent scan mode speeds up.

Components

· The Lumencor SPECTRA Light Engine® (shown in its working position; upside down)

· The adapter; with heat barrier filter and concentrator lens

· The flange with bayonet lock mechanism (the Lumencor light source adapter)

On the rear

Power connector, power switch and power LED

Trigger input (TTL)

Control input of the light engine (RS-232)

Detailed information about features, precautions, warnings and technical data can be found in the file “Lumencor_Spectra_LE_User_Manual.pdf”

Lumencor-White-Paper.pdf

Created wavelengths

The light modules in the lumencor SPECTRA light engine, delivered by 3DHISTECH, creating the excitation lights with the wavelengths as shown on the right.

To excite the fluorophore of the tissue, the light wavelength, selected in the Lumencor SPECTRA, the characteristic of the quad band filter (or the single band filter) and the exciting wavelength of the fluorophore must meet each other, otherwise, the fluorophore will not be excited, the exposure time rise up and the quality of the scanned tissue becomes bad.

How does it work?

Light Engine Subsystem

Each light engine consists of a lamp and delivery optics. The lamp subsystem embodies multiple modules optimized to each produce a precise set of wavelengths. One such module is shown on the right. Here Lumencor’s light pipe technology is the source. Light is generated by a luminescent light pipe which is driven by an e-beam, LEDs or UV lamps. The pipe, which may consist of any of a variety of luminescent materials (e.g. rare earth doped glass, organic doped plastic, single crystal ﬁber) is tailored to emit light in the UV through the NIR. In the case of the rare earths, emission is inherently narrow due to their atomic-like energy structure. Any unwanted light is removed by a simple bandpass filter. The light output from the pipe is fed into an optical delivery pipe and into the instrument. The fast luminescence decay results in rapid switching with no appreciable warm up time.

The light pipe geometry integrates a significant fraction of the light leading to high external efficiencies.

These efficiencies are optimized by the innovative design of the lamp module including the excitation source and the unique geometric shape of the pipe. Increased power levels, exceeding those typical for lasers in these applications, can readily be obtained by scaling the light pipe and associated excitation.

Source: Lumencor-White-Paper.pdf (stored)

Watch slide show: Lumencor SPECTRA light engine

Routing of the light beam

· The Lumencor SPECTRA creates the excitation light by using light modules; each module creates the light in the specified wavelength and the excitation beams are routed by the use of dichroic mirrors.

The modules are switched on or off separately, controlled by the scan program via the control input of the light engine, so the required light wavelength to excite the appropriate fluorophore of the tissue can be created and selected.

Dichroic mirror

A dichroic mirror reflects the lower wavelength of the light while the higher wavelength passes thru it. The edge wavelength keeps the border between lower wavelengths and higher wavelengths.

Dichroic beam splitter (Semrock)

Powering and cabling

P250

The lumencor SPECTRA get its power of 24V- 5A DC from the internal power supply tdk-Lambda of the scanner P250.

Because the relays of the power distribution and switch board can not handle the required current of 5A DC, a Power amplifier is used; it is situated in the common housing of the power supply and the switch board.

Remark

The real working position of the Lumencor SPECTRA Light Engine® is upside down!

External power supply

If the Lumencor SPECTRA Light Engine is used together with the PSCAN or the PMIDI, the shown external power supply is used.

Control of the light engine

The control of the light engine is realized via the RS-232 input; on the other end of the cable an USB 2.0 A-type header is connected.

The control and selecting of the appropriate light wavelength is realized via an USB-port.

The cable header RS-232 contains the converter logic to convert the interfaces from USB2.0 to RS-232 and vice versa.

· If the control cable was exchanged or another USB 2.0 port (on the computer) is used, the USB port address has to be checked and probably updated.

Check and update the USB port address.

Triggering

The trigger cable is connected to the TTL port of the lumencor SPECTRA.

If the shutter of the PCO camera is open, the selected light module (selected via the USB port) will be switched on.

“PCO.edge camera”

Remark

The extension to the RGB BF illumination unit is used in the PCON only!

PCON

The principle of triggering is the same as for the P250 but cable headers are modified!

The trigger output 4 of the camera is used to trigger the RGB illumination unit also.

Control, cables and connections

Check and update the USB port address

Because the control of the light engine is done via an USB 2.0 port of the computer, the scan software has to know the port address.

The port address is defined in the section [Lumencor] of the file “MicroscopeConfiguration.ini”.

If the control cable was exchanged or another USB 2.0 port (on the computer) is used, the USB port address has to be checked and updated.

Start the “Device manager”

· Press “Start”(1), “Computer”(2), “System properties”(3),and “Device Manager”(4).

Find the USB control port address

By connecting or disconnecting the USB connector, the state of the item “USB serial port (COMxx)” is changed.

It is shown in the section “Ports (COM & LPT)” of the device manager; in this example the COM port address 34 is found.

Update the section [Lumencor] of the file MicroscopeConfiguration.ini with the found address:

C:\ProgramData\3DHISTECH\SlideScanner\MicroscopeConfiguration.ini

If the section [Lumencor] does not exist in the file MicroscopeConfiguration.ini (e.g. the Lumencor SPECTRA light engine is implemented later or implemented as a result of upgrade) please create this section.

If the section [Lumencor] is missed

Please implement the following two lines at the end of the file “MicroscopeConfiguration.ini” with a text editor, like “Notepad”:

[Lumencor]

COMportNr=xx

Save the file “MicroscopeConfiguration.ini” without any formatting information, as a *.txt-type file (text only)!

Lumencor table

C:\ProgramData\3DHISTECH\SlideScanner\LumencorTable.csv

The lumencor table is used in the software version 1.15 only to assign exciting light wavelengths to the logical and physical filter positions. The logical filter position means a color channel while the physical filter position defines the position of the filter in the filter wheel of the turret unit.

In the example, only 1 filter block is inserted in the filter wheel position 1.

If a quad band filter is inserted (as shown), it has four color channels; therefore, the logical filter positions from 1 to 4 are used.

In this construction, each color channel occupies a physical filter position also, but the filter wheel stays always in the position 1; so the filter wheel will not move.

The next filter block may be inserted in the filter position 5 of the filter wheel, if required.

Important

· If modifications are done in the file “LumencorTable.csv” the file content has to be saved as txt-type file, without formatting information!

Setup sequence of the Lumencor SPECTRA

Mount the lumencor SPECTRA light engine (see also the Lumencor light source adapter).

Connect the cables (Trigger, RS-232 and power) and switch on the light engine.

Check and update the USB 2.0 port address

Setup filters

Setup filters

For technicians, sales managers and users

In this chapter, the settings are shown for a quad band filter and the software version 1.16 or higher.

· This chapter is true for P250, SCAN and MIDI type scanners.

Start the scan program SlideScanner.exe

In the selector menu, open the option “Microscope Settings”.

The wavelengths of the filter are shown on the label.

DA= DAPI; FI= FITC; TR= TRITC and CY5 = CY5.

For filter sets, filter blocks and filter characteristics, see also: (Links refer to P250)

“Filter block”, “Introduction to fluorescent filters”, “Filter block assembling”, “Cleaning optical filters” (Semrock), “Staining”, “Virtual tissue” and “Fluorescence microscopy”.

“Matching Fluorescent Probes with Nikon Fluorescence Filter Blocks”; interactive

Assign colors, color channels, and filter positions

In the software version 1.15

Because the quad band filter allows the use of 4 colors (color channels) in one physical filter position, the next 3 filter positions, until position 4 can not be equipped with a filter; they are empty positions. In other words, one quad band filter occupies 4 physical positions of the filter wheel.

The next filter block can be inserted in the position 5.