BIOphysics & SOFT Matter Department of Ultrafast Optics and Nanophotonics

Institut de Physique et Chimie des Matériaux de Strasbourg

[No group meeting scheduled]
100%x200

Almost all mechanical parts have been designed and fabricated by Nicolas Beyer @ IPCMS. The magnets: 2 cubes (5 mm) separated by 1 mm. Photograph from mid-2017.

100%x200

Allan deviation (i.e. noise at a given bandwidth) along z (perpendicular to the glass surface) for a 3 micron bead (melted). 126 nm per pixel. 400 Hz. No drift correction. Here, the enclosure was open and there is some acoustic noise contribution.

Software

A custom made Labview software (using a X64 CUDA DLL for the main tracking routine) allows to track tens of molecules at hundreds of Hz and detect sub-nn displacements in real-time. The CUDA code we use is based on the one written by Shawn Tabrizi (GitHub) when working in Saleh's Lab at UCSB (based on Vincent Croquette's work). One of our Internship students (Zhenxiang Luo, now at IMEC) helped ST to run it on X64 platforms and we did additional tweaks (e.g. Flat-Field correction). Recently, Olivier Betschi (doing a 2 months internship in summer 2018, M1 INSA) interfaced our Hardware (camera, Piezo) in Python and wrote the code to call the CUDA DLL in Python. In the next few months, we will fully automize the MT device (injection of beads, recognition of (good) DNA beads, injection of relevant proteins).

Our current GPU is a MSI GeForce GTX 1060 Gaming X 3G allowing to track +50 beads (ROI: 64^2 pixels) at 400 Hz on large images (e.g. 2000 x 2000 pixels). The analysis is performed in real-time (all directions). As we use a buffered acquisition (using a Silicon Software frame grabber), there is no loss of frames.

Softwares (Python or Labview) calling the CUDA DLL and demonstrating tracking are available upon request (wilfried.grangeipcms.unistra.fr).

List of parts

DescriptionSupplierProduct#
95 mm Construction RailTHORLABSXT95-750
Custom plate for Construction Rail
Rail Plate for 95 mm RailsTHORLABSXT95P12/M
Rail CarrierNEWPORTCXL95-80
Superluminescent DiodeSUPERLUMSLD-mCS-261-MP2-SM
Fiber Out-couplerTHORLABSPAF-X-2-B
XY Stage for FiberTHORLABSST1XY-A/M
Post for StageTHORLABSRS75/M
Spacer for PostTHORLABSRS2M
Lens tube spacerTHORLABSSM1T20
FiberPort AdapterTHORLABSCP08FP/M
Translation StagePHYSIK INSTRUMENTEM-126.PD1
Controller for M-126.PD1PHYSIK INSTRUMENTEC-863.11
Rotation StageNANOTECST4118M1804-L
Controller for ST4118M1804-LNANOTECSMCI33-1
EncoderNANOTECNOE2-05-K10
Power SupplyNANOTECNTS-24V-2A
XY Stage for MagnetsTHORLABSST1XY-A/M
Post for StageTHORLABSTR30/M
MagnetsSUPERMAGNETEW-05-N50-G
Custom Adaptor Plate
ObjectiveOLYMPUSUPLFL 100XOI
PIFOCPHYSIK INSTRUMENTEP-726.1CD
PIFOC ControllerPHYSIK INSTRUMENTEE-625
Broadband Dielec. MirrorNEWPORT10D20BD.1
Mirror MountTHORLABSPOLARIS-K25S4/M
45 Degrees AdaptorTHORLABSPOLARIS-MA45/M
ColumnNEWPORTM-PS-1
Imaging LensTHORLABSAC508-200-A
CameraBAUMERHXC-13
Camera Link Add. CableBAUMER11008811
Acquisition cardSILICON SOFTWAREmicroEnable IV AD4-CL
Custom Enclosure SystemMiSUMi
2" Diameter Lens TubesTHORLABSSM2LXX
Lens Tube CouplersTHORLABSSM2TXX
Misc. Hardware (forks etc)THORLABSxx
Honeycomb Optical Table TopSTANDA1HT08-10-20-001
Vibration Isolation SystemSTANDA1VIS10-05-07-70
Syringe PumpHARVARD ApparatusPHD 2000
Sound absorbing panelsAMAZONB00WE8AOPW