Detection

The detection system consists of camera, lens and scintillator screens. Below we list of all the camera, lens and scintillator screens options available at 2-BM.

These are the computers supporting detectors at 2-BM:

Station

Name

Model

Product No.

Serial No.

Manual

2-BM-A

pg10ge

HP Z8 G4

3GF37UT#ABA

pg10ge label

pg10ge SM

2-BM-B

lyra

HP EliteDesk 800

P4K18UT#ABA

lyra label

lyra SM

2-BM-B

tomdet

Super Micro

tomdet label

For each machine part list at purchase time and for the list of supported hardware enter the serial numeber in the HP support web page.

These are the model/part number of the cameras in use at 2-BM:

Cameras

Camera

pixels (HxV)

pixels size (μm)

bit

fps

Manual

Part number

Images

Purchase orider

Grasshopper3 9.1 MP Mono USB3 Vision (Sony ICX814)

3376 x 2704

3.69

14

9

camera_00001

GS3-U3-91S6M-C

camera_order_00001

Grasshopper3 2.3 MP Mono USB3 Vision (Sony Pregius IMX174)

1920 x 1200

5.86

10

163

camera_00002

GS3-U3-23S6M-C

camera_order_00001

Grasshopper3 5.0 MP Mono USB3 Vision (Sony Pregius IMX250)

2448 x 2048

3.45

10

75

camera_00003

GS3-U3-51S5M-C

camera_order_00001

PCO DIMAX HS4 (*)

2000 x 2000

11

12

100 (2277)

camera_00004

camera link

dimax_01 dimax_02 dimax_03

PCO EDGE 4.2 (*)

2048 x 2048

6.5

16

100

camera_00005

camera link

Adimec 12 MP (**)

4000 x 3000

5.5

8

187

camera_00006

Quartz quad CoaXPress Q-12A180 CMV12000

camera_order_00003

Oryx 5.0 MP Mono 10GigE (***)

2448 x 2048

3.45

8-12

162

camera_00007

ORX-10G-51S5M-C

flir flir

camera_order_00002

Oryx 31.0 MP Mono 10GigE (***)

6464 x 4852

3.45

8-12

26

camera_00008

ORX-10G-310S9M

flir

camera_order_00004

Viewworks VNP-604MX-M6H00 (SONY IMX411) (****)

14192 × 10640

3.76

11-16

6.2

camera_00009

VNP-604MX-M6H00

pco.edge 10 BI CLHS (*****)

4432 × 2368

4.6

16

120

camera_00010

10 BI CLHS

camera_quote_00001

Teledyne Kinetix 10

3200 x 3200

6.5

8-12-16

498

camera_00011

O1_KINETIX_10MP_PCIE

camera_quote_00002

(*) use MicroEnable IV VD4-CL

(**) use Euresys Quad-G3 CXP framegrabber

(***) use Myricom ARC Series C-Class Network adapter

(****) use Euresys Coaxlink Quad CXP-12 framegrabber

(*****) use Kaya Instrument Komodo II Camera Link

fps () Only applies to detector with on board memory, transfer speed to on boad memory.

Different combinations of camera, lens and scintillator screensare are possible allowing for flexible data collection speed, pixel size, resolution and field of view. Here are few examples:

Pixels (H)

Pixels (V)

Detector pixel size (μm)

Lens Mag

Sample pixel size (μm)

H filed of view (mm)

V filed of view (mm)

2448

2048

3.45

2

1.73

4.22

3.53

2448

2048

3.45

5

0.69

1.69

1.41

2448

2048

3.45

7.5

0.46

1.13

0.94

2448

2048

3.45

10

0.35

0.84

0.71

2448

2048

3.45

20

0.17

0.42

0.35

2448

2048

6.5

2

3.25

7.96

6.66

2448

2048

6.5

5

1.30

3.18

2.66

2448

2048

6.5

7.5

0.87

2.12

1.77

2448

2048

6.5

10

0.65

1.59

1.33

2448

2048

6.5

20

0.33

0.80

0.67

Oryx

31 Mpixel or the

To use the Flir Oryx camera ORX-10G-310S9M or ORX-10G-51S5M installed at 2-BM-B and connected to tomdet:

[user2bmb@parcturus]$ start_epics

then select Scan/Admin from:

tomo_user

to obtain the FLIR Oryx areadetector main control in the mct_main screen select:

tomo_user tomo_user

To collect an image press Acquire Start.

Startup

To start/stop the area detector IOC for the FLIR Oryx camera ORX-10G-310S9M or ORX-10G-51S5M cameras login into 2bmb@tomdet then type:

[2bmb@tomdet]$ bash
(base) 2bmb@tomdet ~ $ 2bmbOryx5mp
Usage: 2bmSP1.pl {caqtdm|console|edm|imagej|medm|phoebus|remote|restart|run|start|status|stop|usage}

[2bmb@tomdet]$ bash
(base) 2bmb@tomdet ~ $ 2bmbOryx31mp
Usage: 2bmSP1.pl {caqtdm|console|edm|imagej|medm|phoebus|remote|restart|run|start|status|stop|usage}

Manuals

Point Grey

To use the Point Grey GS3-U3-23S6M-C installed at 2-BM-B and connected to lyra:

[user2bmb@lyra]$ start_mona

then select MONA/User/detectors/Point Grey camera (PG3) to obtain the Point Grey areadetector main control screen:

tomo_user

To collect an image press Acquire Start.

Startup

To start/stop the areadetector IOC for the Point Grey (model GS3-U3-23S6M-C) camera login into user2bmb@lyra then type:

[user2bmb@lyra]$ 2bmbPG3
 Usage: 2bmbPG3.sh {start|stop|restart|status|console|run}
[user2bmb@lyra]$ 2bmbPG3 status
[user2bmb@lyra]$ 2bmbPG3 start

Manuals

Adimec

The Quartz quad CoaXPress Q-12A180 CMV12000 installed at 2-BM-A is using the Euresys Quad-G3 CXP framegrabber.

To use the Quartz quad CoaXPress Q-12A180 CMV12000 connected to chiwawa-113, start the Adimec areadetector main control screen

Old version:

[user2bmb@chiwawa-113]$ cd /local/epics/areaDetector-3-2/ADCoaxLink/iocs/coaxLinkIOC/iocBoot/iocCoaxLink
[user2bmb@chiwawa-113]$ ./Start_Adimec_Display.sh
[user2bmb@chiwawa-113]$ ./Start_Adimec.sh
tomo_user

New version:

[user2bmb@chiwawa-113]$ cd /net/s2dserv/xorApps/PreBuilts/areaDetector-R3-10/ADCoaxLink/iocs/coaxLinkIOC/iocBoot/iocCoaxLink/softioc/
[user2bmb@chiwawa-113]$ ./Adimec.sh
  Usage: Adimec.sh {start|stop|restart|status|console|run|medm|caqtdm}
  Additional options:
  Adimec.sh start {screen|procServ|ps|shell}
tomo_user

Startup

To start/stop the areadetector IOC for the Quartz quad CoaXPress Q-12A180 CMV12000 camera login into user2bmb@chiwawa-113 then type:

[user2bmb@chiwawa-113]$ cd /net/s2dserv/xorApps/PreBuilts/areaDetector-R3-10/ADCoaxLink/iocs/coaxLinkIOC/iocBoot/iocCoaxLink/softioc/
[user2bmb@chiwawa-113]$ ./Adimec.sh
  Usage: Adimec.sh {start|stop|restart|status|console|run|medm|caqtdm}
  Additional options:
  Adimec.sh start {screen|procServ|ps|shell}

Old version:

[user2bmb@chiwawa-113]$ cd /local/epics/areaDetector-3-2/ADCoaxLink/iocs/coaxLinkIOC/iocBoot/iocCoaxLink
[user2bmb@chiwawa-113]$ ./Start_Adimec.sh

To collect an image press Acquire Start.

Manuals

Note: Adimec cameras are usable with all Genicam compliant framegrabbers and their GUI software. The Euresys software called EGrabber avaialble at download.

Viewworks 604MP

Test at txmthree:

(base) usertxm@txmthree ~ $ conda create -n egrabber python=3.9
(base) usertxm@txmthree ~/egrabber $ conda activate egrabber
(egrabber) usertxm@txmthree ~/egrabber $ pip install harvesters
(egrabber) usertxm@txmthree ~/egrabber $ conda install -c conda-forge tifffile
(egrabber) usertxm@txmthree ~/egrabber $ python A3_Hardware_Trigger_v1.3.6_BM_async.py

Camera browser:

(egrabber) usertxm@txmthree ~/egrabber $ /opt/euresys/egrabber/bin/x86_64/genicam-browser
tomo_user

Lenses

These are the model/part number of the microscope objective available at at 2-BM:

Brand

each

Part Number

Magnification

WD (mm)

NA

Mitutoyo

3x

NT-46-142

2x

34

0.055

Mitutoyo

3x

NT46-143

5x

34

0.14

Mitutoyo

3x

NT66-383

7.5x

35

0.21

Mitutoyo

3x

NT46-144

10x

34

0.28

Mitutoyo

2x

NT46-145

20x

20

0.42

The purchase record can be found at lens_order_00001, lens_order_00002, lens_order_00003.

Scintillators

Source

Type

Thickness (μm)

Size (mm)

Specification

Order Ref.

ESRF

GGG:Eu

2

8 x 8

esrf1_specs

esrf1_order

ESRF

GGG:Eu

5

8 x 8

esrf1_specs

esrf1_order

ESRF

GGG:Eu

23

8 x 8

esrf1_specs

esrf1_order

ESRF

LOS:Tb

6

8 x 8

esrf1_specs

esrf1_order

ESRF

GGG:Eu

17

8 x 8

esrf2_specs

esrf2_order

ESRF

GGG:Eu

21

8 x 8

esrf2_specs

esrf2_order

ESRF

GGG:Eu

25

8 x 8

esrf2_specs

esrf2_order

Marketech

LuAG:Ce

100

25.4

marketech_order

Marketech

LuAG:Ce

200

25.4

marketech_order

Crytur

LuAG:Ce

20

10

crytur_order_01

Crytur

LuAG:Ce

25

10

crytur_order_01

Crytur

LuAG:Ce

10

10

glued on 1 mm quartz.

crytur_order_01

Crytur

LuAG:Ce

10

10

glued on 0.17 mm quartz

crytur_order_01

Crytur

LuAG:Ce

50

25.5

crytur_order_02

Crytur cleaning crystal surfaces

  1. use a mixture of HCl:HNO3 =3:2, (to remove Al coatings use NaOH)

  2. rins in DI water

Scintillator emissions

Below are the emission spectrum plots of common scintillator screens:

tomo_user tomo_user tomo_user tomo_user tomo_user tomo_user

CCD Lens calculator

To calculate the pixel size / resolution for an arbitrary lens/scintillator/detector combination you can use the CCD Lens calculator to obtain the following:

tomo_user

Visualization

To view the images collected by the detector press ImageJ on the main beamline control screen:

tomo_user

then make sure the areaDetector plug-in for ImageJ, ImageJ_Viewer, is running select:

tomo_user

and press start at:

tomo_user

To open the hdf files saved by the detector use:

  1. fiji: https://imagej.net/Fiji

  2. hdf: plugin from https://github.com/paulscherrerinstitute/ch.psi.imagej.hdf5

  3. hdfview https://support.hdfgroup.org/products/java/hdfview/

  4. argos https://github.com/titusjan/argos