HIPLM User Manual - About Dominic Lepage
Contents
1. Tholabs ER10 12 Cage rod Tholabs ER12 4 Cage rod Tholabs ER4 4 XY lens mount Tholabs HPT1 1 Mirror mount Tholabs 1 2 Kinematic mount Tholabs KMCP M 1 Best form lens Tholabs LBF254 050 A 3 Best form lens Tholabs LBF254 100 A 1 Translation stage Tholabs LT1 M 1 Breadboard Tholabs MB2025 M 1 Breadboard Tholabs MB3045 M 1 Mounting post Tholabs P1 4 Mounting base Tholabs PB2 M 1 Post Spacer Tholabs PS5 M 1 Mounting base Tholabs SCPB1 M 2 Lens tube Tholabs SM1T20 1 Lens tube Tholabs SM1V05 5 Translation Mount Tholabs SM1Z 2 Translation Stage Tholabs TBB0606 M 1 Kaleidoscope Description Supplier Part No QTY 1 2 Mount post Thorlabs PS3 6 Cage Plate Thorlabs CP02 M 2 MAP1030100 Achromatic Doublet Pair Thorlabs A 1 Aspheric Condenser Thorlabs ACL2520 A 2 Breadboard Thorlabs MB1015 M 1 Rod mount Edmund NT64 915 1 Silica Hex light pipe Edmund NT65 835 1 Fibre setup Description Supplier Part No QTY SMA Collimation Thorlabs F220SMA A SM1 Adapter Thorlabs AD11F 5m Multimode fiber Thorlabs M24L05 1 15 26 Principle of beam homogenization Melem rem 7 1 PINS x Mago n ve Ar f V M O 16 26 Schematics dE 200 00 mm B d2. 0 o o o o o o o o o o o o o o o o o a o o a o o o o o o o o 0 5 0 o o o o o o a a o o o o o o o o 0 o 0 0 o 0 0 0 o A 13 26 Beam homogeniser platform Description The beam homogeniser is a complex module designed to generate a uniform illumination at the field of view of any microscope objective and thus independently of the laser source The functioning is illustrated in the Principle of beam homogenization subsection and goes roughly as follows A A laser source is coupled into the multimode fibre Most lasers have a pseudo Gaussian spatial distribution I x and a sharp angular wavevector distribution 1 The phase of laser beam is almost unique coherent B After the 5m of the multimode fibre independently of the input the spatial distribution I x is a Gaussian defined by the fibre coupler However speckle pollutes the distribution as natural coherent interferences statistically occur The wavevectors of the light are cleaned and is virtually collimated due to the fibre size and the collimation system The phase is now randomized C The rotating diffuser is placed after a lens where the wavevectors are broadened Following the rotating diffuser the spatial distribution is still the same but the wavevector distribution is broadened and the spe
3. 8 Detailed 0000202 0 S DAR DENER 10 OVOF VION LSD 10 12 Beam homogeniser platform 100000000090000 14 TOWER aaa aaa aia 18 maging Mod le 21 Hyperspectral Sm a ENE 23 Appendix 1 2 1 12 2 2 1 2 2 212 2 2 2 2 ee 2 25 Adding EE Sanse ARO RO ES 25 Adding the Camera gt 41214 hesek Deke SEAR 25 CONE 25 26 26 Cube rectification HIPLM User Manual Introduction General introduction to the hyperspectral system The hyperspectral photoluminescence mapper HIPLM is a specially modified microscope system The instrument captures 2D images of a sample XY image spectrally dispersed in a 3 dimension as a function of the collected light s energy E The final images produced by the system are stored within a cube of data generating a hyperspectral cube in which each volume pixel voxel corre
4. Ss 0 0000 0 600909 p bop o 4B 000004 li o o o 6008008 00006 4p C boo o o 0 9 o 9 o o o o 17126 Microscope tower Description The microscope tower is where an important fraction of the HIPLM optics takes place When using the system for PL the homogenized light pump comes at the top and passes through a hot mirror or cold for other uses located in the cage cube The pump reaches the microscope objective MO in place where the transmitted light is homogeneous at the focal point of the MO The emitted PL is collected by the MO and reflected by the hot mirror in place In EL mode it is recommended to use a silver mirror for a flatter broadband response Appropriate filters are placed at the exit of the cage cube such as laser and thermal filters and are indicated by the blue arrow in the schematics The PL signal is then sent to the Imaging module Common users have access to the lower section of the Microscope tower through two doors placed in the environmental box Users can change the MO by rotating the objective turret and posi
5. 4 Lens tube Thorlabs SM1L03 3 Translation Mount Thorlabs SM1Z 1 Description Supplier Part No QTY Angle plate Thorlabs AP90 M 1 Goniometer Thorlabs GNL10 M 1 Breadboard Thorlabs MB1515 M 1 Translation stage Thorlabs PT1 M 1 Linear amp Rotation stage Thorlabs XYR1 M 1 19 26 Schematics 200 00 mm or 77 20 26 Imaging module Description The imaging module is accessible through the side of the environmental box This platform is where the imaging plane at the camera is decided between normal imaging for standard XY mapping or conjugate imaging mapping This later mode is employed for the construction of the dispersion relation in I E ky ky of any light scattered under the MO As described in the previous section there are two critical items in this module The first one is the imaging mirror indicated by the blue arrow in the schematics This mirror is positioned at a focal point of both the normal and conjugate imaging modes i e a real image is visible when placing a lens paper on this mirror While this is useful for alignments it is an important source of noise in the measured signal PL EL or Fluo if this mirror is scratched or dusty it will show in the collected data The second important part on this floor is the kinetic mirror indicated by the red
6. All the sources are finally coupled into a multimode optical fibre not shown and led to the Beam Homogenizer To switch between light sources to another open the side of the environmental box and select the kinetic mirror corresponding to the desired light source List of parts Description Supplier Part No QTY Flipper mount Newfocus 9891M L 3 Thread adapter Thorlabs AP6M4M 3 Height spacer Thorlabs BA2S7 M 4 Mirror Thorlabs BB1 E02 8 Height spacer Thorlabs CLCPB1 M 4 Cage plate Thorlabs CP08 M 4 Cage rod Thorlabs ER6 4 Laser filter Thorlabs FL532 10 2 Mirror mount Thorlabs KCB1 1 Mirror mount Thorlabs KS1 4 Mounting base Thorlabs LCPB1 M 4 Post mounting Thorlabs MA4 M 4 Breadboard Thorlabs MB6090 M 1 Mounting base Thorlabs PB2 M 7 Lens tube Thorlabs 5 1105 2 Lens tube Thorlabs 5 1 20 1 DPSS Laser 1 Viasho VA II N 532 1 12 26 Schematics 3 si i gt 0 Lh 23 o o 0 o o o o o o 0 4 H i o ga a or o 5 Of 0 0 O a o o o Do 5 o o o o o o 0 o o 0 a o o a o o o o o o o o o o o o 0 0 0 0 0 x ES e Wy o
7. Video mode for a continuous image feed Automatic Select the automatic acquisition mode in the Apogee acquisition window Specify the wanted wavelength limits and step for your acquisition On the Exposure tab specify the exposure time for your images Input a cube name for the acquisition run Press Start to launch the acquisition sequence Cube rectification Upon completion of an automatic acquisition a full unrectified cube it is necessary to rectify it in order to produce a practical hyperspectral image To do so right click on the data button Data tab gt Cube name and select rectify After rectification it is important to save your data by exporting them menu File gt Export 26 26
8. data File Export Cube o Export the Rectified data same window o Savethe Dark Image Open the dark image display File Save Image e Optional Post processing steps o Refer to the PHySpec user manual for the post processing capabilities of the software 3B Multiple hyperspectral measurements LabView program e Align sample and adjust focus described previously e Evaluate optimal acquisition parameters described previously e Close PHySpec e Open the LabView program e Load the latest calibrations files if not done previously e Setup the acquisition parameters in the Acquisition Window e Specify the output folder e Start the acquisition 3C Real Time hyperspectral snapshots Matlab program e Align sample and adjust focus described previously e Evaluate optimal acquisition parameters described previously e Before closing PHySpec setup the HI wavelength to the desired central wavelength e Close PHySpec e Open the Matlab program e Setup your acquisition parameters e Start the acquisition Step 3 General Closing procedure Put on clean nitrile gloves e Remove all samples and liquids from the HIPLM stage e sure to properly clean all spills e Check the workstation for samples or garbage and make sure to dispose of your tools samples and liquids and to clean the workstation for the next user e Close ALL the box doors correctly e Check that all the fragile equipment is correctly powered o
9. optical filters if required by the operating mode Reinstall the goniometer on the XYO stage Angular Alignment Changing the beam splitter requires a simple realignment of the system in order to have the microscope objective image projected appropriately on the CCD Put on clean nitrile gloves Turn on the white light lamp and place a white paper sample on the stage Do a rough positioning and focus of the paper sample at 760nm for example Switch the system s imaging mode to Conjugate Space easier to align Using an appropriate Hex key loosen the four screws of the beam splitter cap but do not remove them completely loosen by about half a turn to a turn Using your hand turn the beam splitter cap about 1 8 of a turn 452 in either direction This should bring the cap to a position where it will be possible to remove it by sliding it out Slide out the beam splitter cap and its attached beam splitter mirror Be careful to have a linear lateral movement perpendicular to the cap to prevent the optical component to touch the side of the beam splitter box Take the new beam splitter cap and new optical component mirror or beam splitter and insert them in the beam splitter box preventing the optics to touch the box s sides Rotate the cap assembly of about 45 degree until the image is back within the CCD field of view using the Video Mode Carefully align the white visible circle within the frame of the image The center of the c
10. variance of about 150 Close the laser shutter e Once your acquisition time is determined acquire a dark image measurement This single image is used to get the average background noise of the CCD 0 O O O Select the Dark acquisition mode Adjust the exposure time identical to the final measurements Select the number of images to acquire in order to obtain the camera thermal background noise profile the images will be averaged Usually the shorter the exposure the higher this number will be Below a 5 sec exposure we suggest at least 11 to 21 images At longer exposure reduction to about 3 5 is tolerable Save the Dark Image In the image display select File gt Save Image 3A Single Measurement PHySpec e Align sample and adjust focus described previously e Evaluate optimal acquisition parameters described previously e Load the latest calibrations files if not done previously e Proceed with your sample acquisition O O OQ Q O Select the Automatic acquisition mode Setup the desired acquisition wavelength range and step size between images Setup the acquisition time Specify the cube name and description details Open the laser shutter Start the acquisition 4 26 o Upon completion of the acquisition close the shutter e Export data o Right click on the cube name and rectify the cube o Right click on the cube to get a preview of the rectified cube in PHySpec o Optional Export the RAW
11. HIPLM User Manual general user guide By Dominic Carrier amp Dominic Lepage Last updated 1515 September 2012 1 0 Table of contents Introductions initio 1 General introduction to the hyperspectral system eese 1 Hyperspectral imaging 1 Conjugate Space 2 00002 0 0 2 User Manual Common 5 aa vase LEVE HEEL 3 Step 1 General Start up Procedure 3 Step 2 Procedure for Spatial Imaging enne reg 3 Step 3 General Closing procedure EGE aaa 5 Alternative Step 2 Procedure for Conjugate Imaging nnn 6 User Manual Advanced 00000 7 Software Usage and Troubleshooting esses 7 Operating Mode Switch PL EL and FlUO 4 sss sss 8 Routine Alignment ProcedUure
12. are called unrectified images since the x axis is multiplexed with its wavelength content Conjugate Space Imaging For the readers unfamiliar with the Fourier transform and its application in optics the concept could by simplified by stating that instead of observing the spatial disposition of the objects in the image this secondary mode of operation observes at which angle the light is reflected emitted scattered by all the object in the image The polar and azimuthal angles of scattering are therefore mapped as a function of energy This mode of operation is therefore quite practical for the direct measurements of the dispersion relation of any light The schematic in figure 3 illustrates this concept Image plane Fourier plane X Figure 3 Schematics of Conjugate space Imaging All the light emitted from specific point the object will collect an image point in the real imaging left whereas all the light emitted from a specific angle from all parts of the object will collect at a specific position in the Fourier plane right d N Object Object 2 26 User Manual Common Tasks Step 1 General Start up Procedure All the procedures of this guide consider that the user is comfortable with the usage of the related software but mostly the PHySpec software as it is necessary in the sample s alignment If not see Appendix 1 for basic details of operation consult the respective software
13. arrow in the schematics When this mirror is in the erect position the light is directly sent to the imaging mirror and a XY map is sent to the hyperspectral imager When the mirror is down the optical path is elongated as to project the Fourier components of the MO to the imaging mirror A conjugate space cartography is then sent to the hyperspectral imager The procedure for conjugate imaging is described in a section above List of parts Description Supplier Part No QTY Flipper mount Newfocus 9892M L 1 Thread adapter Tholabs AP6M4M 1 General clamp Tholabs CL5 2 Cage rod Tholabs ER3 4 Cage rod Tholabs ERA 4 Kinematic mount Tholabs KMCP M 4 Miror mount Tholabs KS2 4 Cage plate Tholabs LCP01 M 1 Cage adapter Tholabs 2 1 Mounting base Tholabs LCPB1 M 1 Breadboard Tholabs MB3030 M 1 Nikon Tube lens Edmund NT58 520 1 Mounting base Tholabs PB2 M 7 Mirror Tholabs PF20 03 P01 5 Post spacer Tholabs 503 4 Post spacer Tholabs 505 4 Post spacer Tholabs RS075 7 Tube Lens Adapter Udes Homemade 1 21 26 Schematics 0 1 1 1 7 MEDIE 1 Ch SE rms eet CE SN 2223 S Zl n o o 9 o o 22 SS 5 22 26 Hyperspectral box Description This last module contains Photonetc Inc hype
14. ckles time averaged 60hz D A kaleidoscope is place at the focal point of a secondary lens which projects a time smoothed spatial Gaussian at the kaleidoscope input The time independent speckle is now in the wavevector space E Atthe kaleidoscope output a spatially distributed flat top 296 illumination is present The phase x k is further randomized The time independent speckle effect is distributed between the two planes spatial I x and conjugate 1 and minimized by the time average F Acollection optics resizes the beam and projects the appropriate object at the back focal plane of the microscope objective A flat top 296 can then be projected at the objective s field of view The translation stage can be moved to take the rotating diffuser and the focusing lenses out of the optical path This will result in a focusing of the light source into a hot spot on the sample This can be employed for laser surface modifications or for alignment purposes List of parts General Description Supplier Part No QTY Rotating diffuser SUSS 60 1105 911 000 1 Acromat lens Tholabs AC254 075 A 1 Acromat lens Tholabs AC254 100 A 1 Thread adapter Tholabs AP25E6M 4 Thread adapter Tholabs APAM3M 2 Thread adapter Tholabs AP6M4M 1 Mirror Tholabs BB1 E02 2 Cage plate Tholabs CP08 M 8 Height spacer Tholabs CPB1 M 6 Cage rod Tholabs ER1 4 14 26
15. cquisition Automatic Manual Parameters Exposure time s Min 18 05 Calibration Expose Video mode Parameters Figure A1 1 PHySpec interface Specific sub windows are opened by selecting the appropriate tabs on the left column and pressing the related button The HI device control is found under Devices 01000132000 the camera parameters under Parameters gt Apogee and the acquisition window under Acquisition Apogee Adding the HI device e Open the communication port under the menu communication This should be done automatically when the program opens and it should detect automatically which port to use e Open the device list and search for devices menu Devices gt Devices list and button Search for devices Again this should be done automatically at program startup Adding the camera e Select menu Camera Add camera e Select the appropriate driver and camera in this case Apogee and Alta U32 respectively HI control e n the Hyperspectral imager control window input the desired central wavelength and press GO to bring the HI grating in the adequate position The display s central line should be centered at the current wavelength if the calibrations are accurate 25 26 Acquisitions Manual Select the manual acquisition mode in the Apogee acquisition window Move the grating to the desired position Select the exposure time Press Expose for a single image press
16. ff o Laser s o White light lamp o Peristaltic pump o Lasershutter is on the closed state or turned off e Log offthe system and inscribe details in the logbook 5 26 Alternative Step 2 Procedure for Conjugate Imaging As mentioned in the introduction the HIPLM system allows for the imaging of the conjugate Fourier space of an image thus allowing the direct observation of the angular emissions of a sample The procedure to do so is as follow and supersedes or adds to the previously defined Step 2 Procedure for Spatial Imaging The following procedure is a guideline only and you should consult the laboratory manager prior to engaging in any conjugate imaging experiments Refer to the Imaging module schematics for more information 1 Sample Alignment and Focus The sample alignment and focus steps are exactly identical to the procedure described in the spatial imaging section As the conjugate imaging is non trivial alignment and focus in the conjugate space is a challenge at best so those steps are done in the real space before switching to the Fourier space Added Imaging Mode Switch After the sample is aligned the trained HIPLM operator will switch the system from the Spatial imaging mode to the Angular imaging mode Consult the Switching the Imaging Mode from Real to Fourier Space section 2 3A 3C Parameters evaluation and Image acquisition Once the switch in operation mode is completed from this point on the
17. ircle should coincide as much as possible with the center of the image o To align vertically only carefully rotate the cap assembly within the beam splitter box socket Slight movement will have a amplified effects so a minute manipulation is required o To align horizontally you will have to pull out the assembly and adjust the mirror s inclination in relation to the beam splitter cap Great care must be taken so that the surface of the mirror coincides with the center of the beam splitter cap so that the 9 26 projected image is centered on the optical axis before but also after the beam splitter assembly e Once adequately aligned hold the cap in place with one hand while you tighten back the screws to fix the cap assembly back in place e Verify that the alignment is still adequate after tightening the screw Correct if necessary e Close the while light lamp and remove the white paper sample e Switch the system back to the Real Space imaging mode e Proceed with a full spectral calibration mandatory Detailed description Overview Description Due to its multipurpose applications the HIPLM system is composed of several modules which can be adjusted independently Each of those modules is to be aligned on their own and between themselves if the system falls out of alignment The system is divided into five modules First the Laser floor where all the light sources are installed The light pump used for PL or fluorescence is
18. ks the user to proceed the program is ready to work e Consult the Matlab scripts documentation for its specific usage Troubleshooting Those steps describe ways to reinitialize the system to a known and working condition in the case a software problem arises They should be done IN THE SPECIFIED ORDER as the risk of damaging or misaligning the system increases with each step e the HI imager the camera the shutter control or the Voltmeter did not add correctly verify that the equipment is correctly powered on try to restart the application e If the problem persists try to reboot the computer The communication ports may get stuck and a reboot will clear the system s ports e If the problem persists try to power cycle the hardware If accessible use the power button or the power key If the power button is not accessible for the HI and camera use the switch on the power bar to cut down the power for about 15 seconds before activating it again be sure to 7 26 choose power bar dedicated to those equipments As the camera and the HI are sensitive equipment they should never be powered down while executing a task e f the problem persists for the HI ask the designated lab technician to do power cycle of the HI using the switch inside the box DO NOT ATTEMPT this yourself The switch is located close to optical components touching them may misalign the system Operating Mode Switch PL EL and Fluo The HIPLM can be
19. letely visible in the image display or appropriately positioned for the experiment Adjust finely the focus using the Z stage to obtain the sharpest image possible of the sample s surface Stop the Video mode of the camera Turn off the white light lamp 3 26 2 Optimal parameters evaluation e Align sample and adjust focus described previously e Before proceeding with the hyperspectral image acquisition it is important to set up the following parameters 0 0 0 Camera binning Set the camera resolution to 16bits Optional Camera temperature control should not be set to below 2 for extended period Lower values will causes condensation and formation of ice crystals on the camera front glass e Determine the appropriate acquisition time 0 O Move the HI grating to the sample s emission wavelength and manually open the laser shutter Adjust the laser power to the wanted value if not already selected Select the Manual acquisition mode and produce a single image exposure Adjust the acquisition time and repeat exposure to obtain the highest intensity without producing image saturation use the cursor tool to check the intensity of the bright zones Saturation occurs at a value of about 27 or 65535 The higher the average intensity of your image the better signal to noise ratio you will get The noise floor is dependant of the camera temperature but it lies around 1200 1400 intensity unit with a typical
20. manual for further details or ask the laboratory manager Log in the system and inscribe details in the logbook Check the workstation for anomalies abandoned liquids samples If required o Safely dispose and clean the workstation o Make note the anomalies in the logbook o Email the lab manager regarding the anomaly Check that all the equipment is correctly powered on Keithley voltmeter o SC 10Shutter control shutter closed o Power bar of the hyperspectral imager and Apogee camera identified o Laser s if required at the appropriate power Follow the laboratory laser safety procedures at all times o White light lamp intensity if required Step 2 Procedure for Spatial Imaging 1 Sample Alignment and Focus Put on clean nitrile gloves Place the sample on the stage under the microscope objective Open PHySpec initialize the system and load the latest calibration files Open the white light lamp up to an appropriate intensity up to half the maximum is good Set the HI to 760nm if imaging in the NIR 760nm is an appropriate wavelength to be able to simultaneously see a large portion of the image with the white light Adjust if imaging in the VIS Start the Video mode of the camera to about 1 sec exposure gives a good trade off between FPS and brightness for most QW samples Roughly adjust the focus to allow the observation of features on the sample or sample holder Move the sample with the XYO stage until it is comp
21. mirror blue arrow 6 26 o Take extreme care to NOT touch the imaging mirror blue arrow Any dust scratch or irregularity WILL BE imaged directly by the camera thus greatly degrading the output image quality e Remove the hand from the system while avoiding the imaging mirror blue arrow e Carefully close the side door of the HIPLM box making sure there is no gap left User Manual Advanced Details Software Usage and Troubleshooting PHySpec v 1 15 1 e Make sure the HI was correctly initialized distinctive noise and status message in the application e sure the camera was added to the software under the menu Camera gt Add Camera selecting the Apogee driver should identify the camera to add or display Already Added e sure the latest calibration files are loaded e Consult the PHySpec software manual for its specific usage LabView Multi Acquisition e All the required equipments are initialized automatically You should hear the HI system initializes buzzing sound of a stage moving to its extrema 3 times and hear the Keithley voltmeter initializes to its pre recorded default configuration with two loud beeps e lf no error were displayed the system should be ready to go e Consult the LabView software manual for its specific usage Matlab Real Time Pseudo Imaging e The scripts automatically initialize and load the required equipments If no errors were displayed on the command prompt and as
22. procedure of parameters adjustment and image acquisition is identical to the previous section Step 2 Procedure for Spatial Imaging subsection 2 3A 3B and 3C Conceptually the image acquisition procedure stays the same even if the image in itself was modified by a switch to the optical light path Details Switching the Imaging Mode from Real to Fourier Space The following steps should be done by trained personnel only as the kinetic mirror is located in the midst of very sensitive optical elements Touching any of those elements may misalign the whole system or produce visual artefacts in the output image Those steps are written here as a reference EXTREME CARE is required e Put on clean nitrile gloves and make sure to button your lab coat s sleeves e Open the side door of the HIPLM box giving access to the homogenization stage and the mirror floor e With the permission of the lab manager slide the right hand OVER the imaging mirror blue arrow in schematics until the index or major finger touches the TOP of the kinematic mirror red arrow in schematics e While holding the mirror mount FLIP DOWN the kinematic mirror red arrow to go from Real Space imaging to Conjugate Space imaging flip up the mirror to come back to Real Space imaging o The kinematic mirror is spring actuated DO NOT let the mirror go freely Use the hand to accompany the mirror all the way down or up while twisting the wrist around the imaging
23. rspectral imager HI and the CCD camera The HI contains two sets of Volume Bragg Gratings VBG which are designed to work from 400 740nm VIS and 740 1000nm NIR respectively The HI enables the spectral spreading of the image on the camera while preserving the XY or kyky dimensions Hyperspectral cubes are then reconstituted with the various software programs presented in the sections above List of parts Due to Non Disclosure Agreements with Photonetc Inc the authors will not specify the system in great detail in this section However it is important for the advanced user and lab managers to know about the following e Input Output tube lenses Nikon Tube lens Edmund partit NT58 520 e Protected silver mirror employed inside the HI e The camera is an ALTA 2 from Apogee the technical sheet is available here 23 26 Schematics 200 00 mm 24 26 Appendix 1 HIPLM control with 5 Apogee camera setup State Action Current angle DIRECTION 0 002 Binning ROI Readout Gain Cooling Binning and ROI Vertical binning Current wavelength rtical binning 2 0 Step size 1 00 Horizontal binning Gratings temperature Sub image Start X Start Y 27 65 Command 0 0 Current grating Width 2184 25 Height 1472 Not on a grating Effective image size Width 728 Height SYSTEM OK Pixel size 6 8 um x 6 8 um 3 Open shutter Auto Close shutter Apogee A
24. s e Carefully remove the optical filters located after the microscope turret and the beam splitter e On the XY stage install the calibration lamp Neon lamp using the provided optical post and screw right below the microscope objective preferably 10x e Over the lamp insert the diffuser and the small sheet of white paper for better diffusion e The Z adjustment should bring the white paper sheet quite close to the microscope objective not more than 5mm to 1cm away out of focus of the objective again for diffusion purpose e Turn on the neon lamp e Open PHySpec e Start the calibration sequence for both gratings using a 10 sec acquisition time and the default settings for CCD and pixel size see PHySpec software manual for details 8 26 o Using a dielectric hot mirror as beam splitter may cause intensity variations in the Neon peaks Those variations may confuse the calibration algorithm Be sure to use the adequate reference calibration file associated to the installed beam splitter mirror Verify the calibration by moving the HI to spectral lines and verifying that the image at that point is centered on the line Suggested lines o VIS grating line A 585 249nm o VIS grating line B 724 25nm o IRgrating line A 743 89nm o IR grating line B 885 09nm Export the calibration files to the latest calibration folder c HIPLM Latest Calibrations Turn off the Neon lamp and remove it from the XY stage Carefully reinstall the
25. sponds to a coordinate in x y E Although this process is conceptually quite simple the technique employed to produce those images rapidly efficiently and with great quality is not as straightforward The hyperspectral measurement process will be explained in the next sub sections Alternatively the HIPLM system installed in the Laboratory for quantum semiconductors and photon based bionanotechnology QS Group possesses a second imaging mode of operation In the normal mode of imaging the images recorded by the camera are direct images of the sample which corresponds to a XY image The second imaging mode called Conjugate space imaging modifies the light s path inside the HIPLM system and allows the camera to observe the angular distribution of the light emitted by the inspected elements kk image instead of a XY image This imaging mode is discussed in last sub section of this introduction Hyperspectral Imaging An hyperspectral image is a collection of greyscale 2D images where each image expresses the intensity distribution of a specific wavelength Instead of taking one intensity image for the whole spectrum as a normal camera would each image is first sent through a special spectrometer in order to separate its energy wavelengths components The result is similar to a Red Green Blue RGB image but with the complete spectrum of probed light instead of only three components The RGB separation is illustrated below in fig
26. then coupled into the second module the Beam homogeniser platform This platform enables a homogeneous illumination of the substrates over the field of view It is also possible to switch the illumination to a single hot spot on this floor The Microscope tower is the third section where most of the collection and injection optics is installed along with interchangeable filters The lower section of the Microscope tower is only sector that should be accessible to the unspecialized HIPLM users The collected PL or EL from this tower is then sent to the Imaging module where the advanced user can switch to the conjugate space imaging for SPR studies The last module consists of the Hyperspectral box containing the Volume Bragg Grating from Photonetc Inc and the Apogee Camera Each module will be discussed in more details in the coming sections 10 26 Schematics 1000 mm 650mm 0000 11126 Laser floor Description The laser floor is designed to support four 4 different illumination sources which can be employed as various PL pumps or fluorescence Each source is coupled to a pair of mirrors mounted on a standard and kinetic flipper mounts Those are employed to align independently each source with the last two mirrors of the laser floor These last two mirrors are aligned with the rest of the system and should NOT be disturbed when installing a new source
27. tion their samples in 200 i e the 3 spatial axis polar and azimuthal angles Not indicated in these schematics are the tubes coming in and out of the peristaltic pump located outside the environmental box Various tubes reach the sample holder and are used to control injection of liquids Also note that operating a mode switch EL PL Fluo or basic angular alignment of the system might involve a change in beam splitter see Operating Mode Switch or Routine Alignment Procedure sections This filter is located in the cage cube indicated by a red arrow in the schematics Follow the procedures described in the previous sections if this is necessary List of parts General Description Supplier Part No QTY Cover plate Thorlabs B1C 1 Rotatable platform Thorlabs B3C 1 Mirror Thorlabs 2 2 1 Thorlabs C4W 1 Cage adapter Thorlabs 7 2 Thorlabs ER4 4 Filter mount Thorlabs 1 1 Mirror mount Thorlabs KCB2 1 Best form lens Thorlabs LBF254 100 A 1 Shorpass filter Edmund NT47 590 1 M O 10x Edmund NT58 516 0 Hot mirror Edmund NT64 469 1 Long pass Edmund NT64 513 1 Objective turret Thorlabs OT1 1 Mounting post Thorlabs P30 M 2 Mounting base Thorlabs PB2 M 4 Post spacer Thorlabs PS3 1 18 26 Stage Base plate Thorlabs PT101 1 Thread adapter Thorlabs RMSA2
28. ure 1 Figure 1 RGB color scheme Conceptual color separation within a full color image Each color is represented with an intensity image where the white color represents a full intensity and a black color represent a total absence of the color at that position Computer uses only three specific colors to represent the commonly used visible color spectrum but as light is a continuous spectrum it can be measured and stored much more precisely in an hyperspectral image The precise optical concepts of the spectrometer and how it works are out of the scope of this document but it is necessary to describe what they output The output image of the spectrometer has 1 26 the same morphology as the input which means that there is direct correspondence between the input and output pixels That said the snapshots produced by the system during the measurements are not an intensity image at a specific wavelength as illustrated in the left part of figure 2 but a continuous image in wavelength along the x axis figure 2 right part Figure 2 Hyperspectral imaging The left part illustrate the final output of the HIPLM system consisting of a sequence of images where each image represent the intensity distribution of the light at that specific wavelength The right part illustrates the snapshot taken by the HIPLM system at a specific central wavelength before post processing into the final hyperspectral image The snapshots
29. used for multiple applications Those applications consist primarily in PL photoluminescence EL electroluminescence and Fluo fluorescence In order to increase the quality of the measurements it is possible to fine tune the utilized optical components to collect more light or filter undesired light The two main optical components to change are the beam splitter and the collection optical filters located after the microscope turret and the beam splitter Since changing between those operating modes requires modifying optical components alignment of the beam splitter and a spectral calibration are necessary after each modification Refer to the schematics of the Microscope tower for more information If necessary e Change beam splitter in cage cube red arrow Hot cold mirror beam splitters etc e Change Optical filters blue arrow Laser filters thermal noise filters VIS NIR filters etc Routine Alignment Procedure Those procedures are destined to the trained personnel in charge of maintaining the HIPLM system They should not be attempted by an untrained user Spectral Calibration The following procedure describes the way to do a spectral calibration and its related calibration files Those are necessary for yielding acceptable precision in the measurement and rectification process of the hyperspectral images e Remove the goniometer from the XYO stage e Make sure the laser shutter is closed e Putonclean nitrile glove
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