{"authors":[{"id":"585192966","orcid":"","email":"","name":"Justin D. Hanselman","affiliation":"Hope College"},{"id":"1570719935","orcid":"0000-0002-5288-3744","email":"kopek@hope.edu","name":"Benjamin G. Kopek","affiliation":"Department of Biology, Hope College"}],"bricks":[{"abstract":"","id":"275576586","functions":[{"id":"2112220587","description":"","implementations":[{"id":"1994175742","quantity":1,"type":"brick"},{"id":"1718413669","quantity":1,"type":"brick"},{"id":"2008397736","quantity":1,"type":"brick"},{"id":"612775392","quantity":1,"type":"brick"},{"id":"1599450779","quantity":1,"type":"brick"},{"id":"1770657789","quantity":1,"type":"brick"},{"id":"1212037556","quantity":1,"type":"brick"},{"id":"171866889","quantity":1,"type":"brick"},{"id":"2074971881","quantity":0,"type":"brick"},{"id":"1494318766","quantity":1,"type":"brick"},{"id":"1922376863","quantity":1,"type":"brick"},{"id":"219949952","quantity":1,"type":"brick"}]},{"id":"195975849","description":"","implementations":[]}],"authors":[],"files":[{"url":".\/.\/usdata\/PhysicalAssemblyBeamSide.jpg"},{"url":".\/.\/usdata\/PhysicalAssemblyCameraSide.jpg"}],"long_description":"Overview of the fully assembled microscope.","instructions":[{"name":"assembly","steps":[]}],"name":"Super-resolution Fluorescence Microscope","license":"CC-BY 3.0","notes":""},{"abstract":"","id":"1994175742","functions":[{"id":"1449739480","description":"","implementations":[{"id":"1854461583","quantity":1,"type":"part"},{"id":"1540219253","quantity":4,"type":"part"},{"id":"1663798749","quantity":4,"type":"part"},{"id":"1970249459","quantity":4,"type":"part"},{"id":"1651425089","quantity":4,"type":"part"},{"id":"1715516067","quantity":1,"type":"part"},{"id":"33719668","quantity":4,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/LaserBoxAndStandAssemblyExploded.png"}],"long_description":"A custom built stand for the laser unit.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Secure the four 25mm Posts (5) to the Laser Stand Plate (3) using four Hex Drive Flat Head Screws (2).","components":[]},{"files":[],"description":"Screw four 31.8 mm Studded Pedestal Base Adapters (6) into the bottoms of the four 25mm Posts (5).","components":[]},{"files":[],"description":"Unscrew the screws that hold the feet of the unit in place. Take care when rotating the unit to not jar it, as this can damage the internal mirror position. Secure the laser unit (1) to the custom laser stand plate (3) using four socket head screws (1\/4\"-20, 1 \" long) (4).","components":[]},{"files":[],"description":"The laser stand unit can be secured in an appropriate location on an optical breadboard. (see overview of microscope system). It may be necessary to add additional height to the Optics Posts due to the uncertainty of height of the raster mirrors in the laser. This can only be verified by ensuring the center of the raster. 25mm Post Spacers can be screwed onto the other Posts to provide the necessary height.","components":[]}]}],"name":"Laser Box & Stand","license":"","notes":"The laser unit should be mounted on a stand so that the beam is able to be projected straight for alignment purposes."},{"abstract":"","id":"1718413669","functions":[{"id":"710088336","description":"","implementations":[{"id":"1651425089","quantity":4,"type":"part"},{"id":"1970249459","quantity":4,"type":"part"},{"id":"1335646361","quantity":4,"type":"part"},{"id":"1558918840","quantity":1,"type":"part"},{"id":"1540219253","quantity":4,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/Vertical-Line-Assembly-Outer.png"}],"long_description":"Main support for the vertical line of the imaging system.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Position Clamping Forks (1) in appropriate location on the optical breadboard (see overall schematic). For spacing, one can use the Translation Stage Mount Plate as a guide.","components":[]},{"files":[],"description":"Slide 31.8 mm Studded Pedestal Base Adapters (2) into Clamping Forks (1).","components":[]},{"files":[],"description":"Screw 25.0 mm Pillar Posts (3) into 31.8 mm Studded Pedestal Base Adapters (2).","components":[]},{"files":[],"description":"Position Custom XY Sample Translation Stage Mount Plate (6) so that holes line up with Pillar Posts (3). Screw Mount Plate (6) to Pillar Posts (3) using Socket Head Screws (6).","components":[]},{"files":[],"description":"Secure Stage (7) into Plate (5) using Flat Head Screws (4).","components":[]},{"files":[],"description":"Position assembly so that internal screw holes match up with the cage system from the vertical line assembly. Use Clamping Forks to secure in place and tighten.","components":[]}]}],"name":"Stage Support Assembly","license":"","notes":""},{"abstract":"","id":"2008397736","functions":[{"id":"585169899","description":"","implementations":[{"id":"42248522","quantity":1,"type":"part"},{"id":"1715353230","quantity":1,"type":"part"},{"id":"1997220404","quantity":1,"type":"part"},{"id":"2079060766","quantity":1,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/Vertical-Line-Assembly-Inner.png"}],"long_description":"","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Before starting, if differential adjuster is not on the correct side of (10) (as pictured), remove the screws and rebolt the differential adjuster hardware on the appropriate side.","components":[]},{"files":[],"description":"Remove the stock differential adjuster by loosening the clamp bolts and then insert the (DM10) Differential Adjuster (11).","components":[]},{"files":[],"description":"Screw 100X objective (8) into Adapter (9) with External SM1 Threads and Internal RMS Threads.","components":[]},{"files":[],"description":"Screw Objective\/Adapter into Translation Stage (10).","components":[]},{"files":[],"description":"Set the Adjuster aside to assemble the cage system.","components":[]}]}],"name":"Objective Mount and Z-Translation Mechanism","license":"","notes":""},{"abstract":"","id":"612775392","functions":[{"id":"1923275626","description":"","implementations":[{"id":"619121990","quantity":1,"type":"part"},{"id":"1004329692","quantity":1,"type":"part"},{"id":"1636443401","quantity":1,"type":"part"},{"id":"245102677","quantity":1,"type":"part"},{"id":"878925890","quantity":1,"type":"part"},{"id":"214211596","quantity":1,"type":"part"},{"id":"1745862721","quantity":1,"type":"part"},{"id":"993412938","quantity":1,"type":"part"},{"id":"161358789","quantity":1,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/0-0-Vertical-Line-Assembly-Inner.png"}],"long_description":"","instructions":[{"name":"assembly","steps":[{"files":[],"description":"To insert the Dielectric Mirror (20) into the Right-Angle Kinematic Mirror Mount (21), loosen the screws and remove the mirror holder. Place the Mirror (20) into the support (use gloves or handle only by edges) and reattach mirror support to the rest of the Mounting unit.","components":[]},{"files":[],"description":"Screw SM1 Coupler (22) into top of Mirror Mount (21).","components":[]},{"files":[],"description":"Screw f=200 mm lens (23) into SM1 coupler (22).","components":[]},{"files":[],"description":"Attach Right-Angle Kinematic Mirror Mount with mirror and lens into the bottom of 30 mm Cage Cube (24).","components":[]},{"files":[],"description":"Mount the 30 mm Filter Mount (26) to the Kinematic Cage Cube Platform (27) using two M3 cap screws.","components":[]},{"files":[],"description":"The Filter Holder has a spring-loaded clamping mechanism. To mount the Dichroic beamsplitter (25), apply a horizontal force to the clamps, insert the beamsplitter into the chanel, and release the clamps. When working with the beamsplitter be sure to use gloves or handle only by the edges.","components":[]},{"files":[{"url":".\/.\/usdata\/Kinematic_Cube_Platform_A1-780.jpg"}],"description":"Attach the Kinematic Cage Cube Platform with attached Filter Holder to the 30 mm Cage Cube using the screws included with the Cube Platform. Look at diagram for correct orientation. Align the mirror so that its notches allow it to go past the screws. Roughly rotate the mirror to be 45 degrees to the horizontal and then tighten the screws until a firm pressure must be used to rotate the mirror any further. The mirror will be adjusted slightly later during laser alignment.","components":[]},{"files":[],"description":"Screw on Dust Cap (12) in appropriate location on 30 mm Cage Cube, referring to diagram for correct orientation.","components":[]}]}],"name":"Mirror and Filter Assembly","license":"","notes":"A variety of filters can be used according to the needs of the investigator and desired excition and emission wavelengths. The parts and filters we describe here are appropriate for excitation and emission of Alexa Fluor 647."},{"abstract":"","id":"1599450779","functions":[{"id":"1652322488","description":"","implementations":[{"id":"1718413669","quantity":1,"type":"brick"},{"id":"612775392","quantity":1,"type":"brick"},{"id":"2008397736","quantity":1,"type":"brick"},{"id":"1150302875","quantity":4,"type":"part"},{"id":"1728764877","quantity":4,"type":"part"},{"id":"1788309638","quantity":1,"type":"part"},{"id":"305044356","quantity":4,"type":"part"},{"id":"1549084167","quantity":1,"type":"part"},{"id":"483424046","quantity":1,"type":"part"},{"id":"159153016","quantity":2,"type":"part"},{"id":"1332802642","quantity":1,"type":"part"},{"id":"207421269","quantity":1,"type":"part"},{"id":"1029968339","quantity":4,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/0-Vertical-Line-Assembly-Inner.png"},{"url":".\/.\/usdata\/0-Vertical-Line-Assembly-Outer.png"}],"long_description":"Assembly of the sample stage, mirror and filter assembly, and objective mount and Z-translation mechanism.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Stage support assembly should be mounted on the breadboard.","components":[]},{"files":[],"description":"Screw the four 4\" long Cage Assembly Rods (28) into top of the Cage Cube of the Mirror and Filter Assembly (24).","components":[]},{"files":[],"description":"Slide the objective assembly (8-11) over the cage rods and then let it sit on the bottom.","components":[]},{"files":[],"description":"Attach the Mirror and Filter Assembly to the bottom of Custom Mount Plate (5) of the Stage Support Assembly using four 0.5\" long Socket Head Screws 4-40 (29).","components":[]},{"files":[],"description":"Attach the Sample Stage (7) to the Aluminum Mount Plate using four M4 x 0.7 mm Socket Head Screws (12 mm long) (4).","components":[]},{"files":[],"description":"Adjust the differential adjuster (12) so that it is midway through its coarse range and fine adjust range.","components":[]},{"files":[],"description":"Raise the objective assembly to a height that allows it to translate at the plane of the sample. This can be determined empiricaly by adding oil to the objective, placing a slide into the holder, and then bringing the objective up to a height where the oil makes contact with the slide. Secure the Objective assembly to the rods using the screws. This can also be adjusted later if needed.","components":[]},{"files":[],"description":"Attach the Motor-to-Differential Adjuster Connecter (13, 14) using Socket Head Screws 8-32 (15).","components":[]},{"files":[],"description":"A Bandpass filter (green or red) can be placed in the Cage Cube below the beamsplitter according to the fluorophore being imaged. The Filters listed here will \"sit\" in the Cage cube. Changing the filters can be somewhat difficult, but can be aided using forceps. Be cautious not to touch the filters with bare hands.","components":[]},{"files":[],"description":"For safety, we cut a small square of black foam board (18) to cover the side of the Cage cube using M3 x 0.5 mm (8 mm long) button head screws (17).","components":[]}]}],"name":"Vertical Line Assembly","license":"","notes":""},{"abstract":"","id":"1770657789","functions":[{"id":"234951831","description":"","implementations":[{"id":"1651425089","quantity":1,"type":"part"},{"id":"1970249459","quantity":1,"type":"part"},{"id":"138472799","quantity":1,"type":"part"},{"id":"33719668","quantity":1,"type":"part"},{"id":"540364524","quantity":1,"type":"part"},{"id":"31738501","quantity":1,"type":"part"},{"id":"743875788","quantity":1,"type":"part"},{"id":"202884993","quantity":1,"type":"part"},{"id":"1636443401","quantity":1,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/Camera-Tube-Assembly-Exploded.png"}],"long_description":"Attaching camera to system.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Thread the Adapter with External C-Mount Threads (7) onto the camera lens.","components":[]},{"files":[],"description":"Attach the SM1 Lens Tube (8) onto the Adapter with External C-Mount Threads.","components":[]},{"files":[],"description":"Attach the SM1 Coupler (9) to the SM1 Lens Tube (8).","components":[]},{"files":[],"description":"Position the Short Clamping Fork (1) at the approximate location specific for ones set-up.","components":[]},{"files":[],"description":"Screw the Post Holder (2) into the Studded Pedstal base (3).","components":[]},{"files":[],"description":"Use the Clamping Fork (1) to Clamp the Studded Pedstal Base (3).","components":[]},{"files":[],"description":"Screw the Adapter (5) with Internal M4 x 0.7 Threads onto the Optical Post (4).","components":[]},{"files":[],"description":"Attach the Adapter\/Optical post to the Camera (6).","components":[]},{"files":[],"description":"Position the Camera by placing the attached Optical Post into the Post Holder. One can adjust to the desired height using the Post Holder with Spring-Loaded Hex Lock.","components":[]},{"files":[],"description":"Align the camera using standard methods.","components":[]}]}],"name":"Camera Line","license":"","notes":"There is a need to align the rough camera position first. It consists of assembling everything else, attaching 2 cage rods where the tubes are, and then using targets with holes at few spaces apart. The kinematic mirror is then rotated to direct at about a 45 degree angle down and the laser is turned on as low power. CAUTION: Wear appropriate laser safety glasses for laser alignment. Glasses can be purchased depending on wavelength. You first want to adjust the the beam angle so that the light is centered on the target holes. Then move each target so that the beams are showing on the edges of the holes. Wherever the beam lines up at the fine smallest point on the solid target in the back, that is the desired location of the camera sensor. You will want to mark the cage or take a measurement and then from there you will pre screw in the two tubes (8 & 9) to the approximate length and slide the camera accordingly. Later for ensuring the camera is in the correct focal plane, you will have a known image (and the mirror in the correct orientation) and will then move the camera in and out until that image focuses."},{"abstract":"","id":"171866889","functions":[{"id":"10704307","description":"","implementations":[{"id":"1300675893","quantity":4,"type":"part"},{"id":"1253581193","quantity":2,"type":"part"},{"id":"1363123240","quantity":1,"type":"part"},{"id":"416675147","quantity":1,"type":"part"},{"id":"1769339429","quantity":1,"type":"part"},{"id":"1506841281","quantity":1,"type":"part"},{"id":"540364524","quantity":1,"type":"part"},{"id":"1065137023","quantity":1,"type":"part"},{"id":"1004329692","quantity":1,"type":"part"},{"id":"619121990","quantity":1,"type":"part"},{"id":"310292384","quantity":1,"type":"part"},{"id":"691502391","quantity":2,"type":"part"},{"id":"1675867349","quantity":1,"type":"part"},{"id":"93878551","quantity":1,"type":"part"},{"id":"1964403163","quantity":1,"type":"part"},{"id":"1178746898","quantity":4,"type":"part"},{"id":"1150302875","quantity":6,"type":"part"},{"id":"1970249459","quantity":5,"type":"part"},{"id":"1651425089","quantity":5,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/Bean-Expander-Assembly-Exploded.png"}],"long_description":"Assembly of components between the laser and Mirror and Filter Assembly.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Attach Cage Plate (2) to Lens Tube Coupler (3).","components":[]},{"files":[],"description":"Attach Extension Tube (4) to Cage Plate\/Lens Tube Coupler from previous step.","components":[]},{"files":[],"description":"Attach other Cage Plate to opposite end of Extension Cube.","components":[]},{"files":[],"description":"Screw two Optical Posts (150 mm) (1) into two Studded Pedstal Base Adapters (18).","components":[]},{"files":[],"description":"Screw Optical Posts with Base Adapters into the Cage Plates on opposite ends of the Extension Tube.","components":[]},{"files":[],"description":"Attach the full Extension Tube Assembly to the Optical Breadboard at the appropriate locations for microscope set-up using Clamping Forks (19).","components":[]},{"files":[],"description":"Insert Dielectric Mirror (10) into Right Angle Kinematic Mirror Mount (9).","components":[]},{"files":[],"description":"Attach one Optical Post (150 mm) into studded Pedestal Base.","components":[]},{"files":[],"description":"Screw Optical Posts with Base Adapter into the bottom of the Right Angle Kinematic Mirror Mount (9).","components":[]},{"files":[],"description":"Attach the Right Angle Kinematic Mirror on the Optical Post to the Optical Breadboard using a Clamping Fork. Attach this to the Optical Breadboard at an appropriate location for your set-up, approximately 4 inches from the end of the previously mounted Extension Tube Assembly.","components":[]},{"files":[],"description":"Screw the Iris Diapraghm (11) onto the XY-translating ring mount (12).","components":[]},{"files":[],"description":"Screw the f=30 mm Achromatic Doublet (13) lens onto the other side of the XY-translating ring mount.","components":[]},{"files":[],"description":"Slide the four Cage Assembly Rods (8\" long) through the XY-translating ring mount.","components":[]},{"files":[],"description":"Screw the f=100 Achromatic Doublet lens (14) onto another XY-translating ring mount.","components":[]},{"files":[],"description":"Slide the XY-translating Ring Mount onto the four Cage Assembly Rods that the other XY-translating ring mount with the f=30 mm lens was already slid onto. Orient the Ring Mounts according to the diagram.","components":[]},{"files":[],"description":"Attach a Cage Plate (15) to the ends of the four Cage Assembly Rods (16) through which the lens are mounted by screwing the rods into the cage plate.","components":[]},{"files":[],"description":"Screw an Optical Post (150 mm) onto a Studded Pedestal Base Adapter.","components":[]},{"files":[],"description":"Screw the Optical Post into the Cage Plate with the Assembly Rods and Lenses.","components":[]},{"files":[],"description":"Screw the free ends of the Cage Assembly Rods of the unit containing the lenses into the Right Angle Kinematic Mirror Mount.","components":[]},{"files":[],"description":"Attach the free Optical Post attached to the Cage Plate to the Optical Breadboard using a Clamp.","components":[]}]}],"name":"Excitation Beam Line","license":"","notes":"CAUTION: Wear appropriate laser safety glasses for laser alignment. Glasses can be purchased depending on wavelength. \n The Beam from the laser needs to be aligned (via angle) to pass through the targets that hang on the cage bars (and don't shift up or down over the distances much). The mirror (10) can be adjusted to achieve a straight beam path down the cage. The first calibration phase involves no beam expanders but just ensure the beam stays in the same spot on the target down the line (and roughly in the middle of the cage.\n After sliding on the beam Expanders and attaching the lenses, you then position the beam expanders far enough apart that the beam on the target does not expand more than the size of the optics (into the second one). The top and bottom screws on the first beam expander can be used to adjust the position of the beam to the middle of the cage. This relative distance should be noted and maintained.\n When connecting this whole thing together, you will then want to move the two lenses closer or further from the mirror so that the most amount of light enters the bottom of the objective without going too far past it."},{"abstract":"","id":"1494318766","functions":[{"id":"1075372608","description":"","implementations":[{"id":"552521340","quantity":1,"type":"part"},{"id":"732866040","quantity":1,"type":"part"},{"id":"433864033","quantity":1,"type":"part"},{"id":"2130531101","quantity":2,"type":"part"},{"id":"305044356","quantity":4,"type":"part"},{"id":"1219524197","quantity":8,"type":"part"},{"id":"122175889","quantity":8,"type":"part"},{"id":"1788309638","quantity":0,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/Chamber-And-Flat-Slide-OWIS-Mount.png"}],"long_description":"Custom designed holder to fit on the OWIS stage. Holds a chambered coverslip.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"3D print parts 1-4 in PLA or more rigid plastic.","components":[]},{"files":[],"description":"Place the compression springs over the threads of eight 25 mm long M6 x 1.0 mm socket head screws. Attach spring clamps to the base using the eight 25 mm long M6 x 1.0 mm socket head screws onto which the compression springs were threaded.","components":[]},{"files":[],"description":"Attach the fully assembled custom coverslip holder to the OWIS sample XY translation stage using M4 x 0.7 mm socket head screws. This may be done after the stage has already been assembled with the rest of the system.","components":[]}]}],"name":"Chambered Coverslip Holder","license":"","notes":""},{"abstract":"","id":"1212037556","functions":[{"id":"548289988","description":"","implementations":[{"id":"1172382293","quantity":1,"type":"part"},{"id":"1947411957","quantity":1,"type":"part"},{"id":"634050904","quantity":1,"type":"part"},{"id":"134265758","quantity":2,"type":"part"},{"id":"430393902","quantity":2,"type":"part"},{"id":"1612010827","quantity":1,"type":"part"},{"id":"1746782452","quantity":4,"type":"part"},{"id":"595388234","quantity":2,"type":"part"},{"id":"1592805244","quantity":1,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/Autofocus-Assembly-Exploded.png"}],"long_description":"Components and assembly of the autofocus system.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Use a Threading tool to thread the center hole of (3) to the adapter thread","components":[]},{"files":[{"url":".\/.\/usdata\/JWWinco-GN 479.1-30-Motor-Bracket.SLDDRW"}],"description":"Drill the appropriate hole according in (3) to screw into base (2).","components":[]},{"files":[],"description":"Thread (3) onto the base (2).","components":[]},{"files":[],"description":"Insert (5) thread inserts into (4).","components":[]},{"files":[],"description":"Slide the assembled screws\/thread inserts (4\/5) into (3).","components":[]},{"files":[],"description":"Match (6) up so that you can see (5) in the T-slot.","components":[]},{"files":[],"description":"Screw (8) loosely into the bottom thread insert.","components":[]},{"files":[],"description":"Position the second screw near the top of the cross cutout and loosely screw into the thread insert.","components":[]},{"files":[],"description":"Tighten the screws until it takes some pressure to slide (6).","components":[]},{"files":[],"description":"Align (9) to match the screw holes with its electrical plug facing away from (3).","components":[]},{"files":[],"description":"Screw (9) into (6) using (7).","components":[]},{"files":[],"description":"Position the pedastal and fork loosely on the breadboard. However, final alignment has to happen after the manual stage is already setup.","components":[]}]}],"name":"Autofocus","license":"","notes":""},{"abstract":"","id":"2074971881","functions":[{"id":"1970156738","description":"","implementations":[{"id":"723684303","quantity":3,"type":"part"},{"id":"1619008330","quantity":2,"type":"part"},{"id":"1373211908","quantity":3,"type":"part"},{"id":"505426117","quantity":8,"type":"part"},{"id":"1225690253","quantity":1,"type":"part"},{"id":"624048646","quantity":1,"type":"part"},{"id":"92882187","quantity":1,"type":"part"},{"id":"1728863779","quantity":2,"type":"part"},{"id":"430587125","quantity":1,"type":"part"},{"id":"451020246","quantity":1,"type":"part"},{"id":"247527998","quantity":1,"type":"part"},{"id":"669233220","quantity":2,"type":"part"},{"id":"942245459","quantity":1,"type":"part"},{"id":"121969198","quantity":3,"type":"part"},{"id":"1326558620","quantity":9,"type":"part"},{"id":"1758160706","quantity":1,"type":"brick"},{"id":"1686616936","quantity":1,"type":"part"}]}],"authors":[],"files":[{"url":".\/.\/usdata\/PowerSupplyBoxAssemblyExploded.png"}],"long_description":"A custom made power supply box for the autofocus stepper motor.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Print the Custom 3D Power Supply Enclosure.","components":[]},{"files":[],"description":"Drill holes in (7).","components":[]},{"files":[],"description":"Attach the AC-DC Converter (5) to the Aluminum Plate (7) using Button Head Screws M3x0.5 (4 mm) (8).","components":[]},{"files":[],"description":"Insert the 3-pin JST SM Plugs (3) into the slots in the 3D printed enclosure. (From the inside of the enclosure)","components":[]},{"files":[],"description":"Secure the Aluminum sheet (7) to the 3D printed plastic enclosure using Button Head Screws M3x0.5 (8mm) (4).","components":[]},{"files":[],"description":"Insert the fuse into the AC Receptacle (10).","components":[]},{"files":[],"description":"Use Button Head Screw M3x0.5 (10 mm) (12) and the Hex Nut M3x0.5 (2) to secure the AC Receptacle to the Plastic Enclosure (9).","components":[]},{"files":[],"description":"Using a Crimp tool and appropriate length of 16AWG wires in the corresponding colors, strip one end and then crimp the Quick Disconnects (1) to the other end.","components":[]},{"files":[{"url":".\/.\/usdata\/PowerSupplyInternalWiring.png"},{"url":".\/.\/usdata\/Inside of Power Supply Box.png"}],"description":"Use 16AWG wire to make connections from the AC Receptacle to the AC-DC Converter. To connect the 24 AWG pigtails to the corresponding terminals of (5) thread the stripped wire ends under the nut and then tighten the screw down","components":[]},{"files":[{"url":".\/.\/usdata\/PowerSupplyCableConnection.jpg"}],"description":"Connect the 16 AWG Disconnects (1) to the AC Receptacle.","components":[]},{"files":[],"description":"Using the male JST SM Plugs and pigtails, strip the ends of the pigtails.","components":[]},{"files":[],"description":"Find the USB-To-Motor Controller boxes' power connector. Strip the wires on the end of the power connector.","components":[]},{"files":[],"description":"Using the crimp tool and the splice connector push the corresponding spliced ends together and then pinch them together. Note: Color codings may not be accurate due to product changes. Please refer to the user manual to ensure that the connected wire at the controller matches the postive 24V (V+) and the 0V (V-)","components":[]},{"files":[],"description":"Plugin the AC power cord. To test the voltage, use a multimeter and the open lid, Press the positive on V+ and negative on V- for DC voltage. If the number is not the desired 24V, turn the screw slowly to adjust the voltage (24 Volts minimizes chances for inaccuracy).","components":[]}]}],"name":"Autofocus Power Supply","license":"","notes":""},{"abstract":"","id":"1758160706","functions":[{"id":"1612145168","description":"","implementations":[{"id":"1289146856","quantity":1,"type":"part"}]}],"authors":[],"files":[],"long_description":"For the chosen stepper motor from Oriental Motor LLC, a driver is required that must be communicated with via RS485 protocol. In order to interface such communication with micro-manager on a PC, a USB To RS485 adapter must be purchased.\n\nThe documentation pertaining to this particular adapter is in regards to the recommended adapter by Oriental Motor. Please note, Oriental Motor requires a custom wiring of Ethernet wires into the adapter. DO NOT order adapters that are simply listed as USB to RS-485, as Oriental Motor uses a non-standard wire configuration into their units.","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Using an appropriate length of Ethernet cable for your setup, run the cable to the computer.","components":[]},{"files":[],"description":"At sufficient length, use wire strippers to cut the cable and peel back the outside cable insulation.","components":[]},{"files":[],"description":"Untwist the wire pairs inside","components":[]},{"files":[],"description":"Verify that the Cable is either TIA\/EIX T-568B or TIA\/EIX T-568A (there are adequate resources online to help you identify this).","components":[]},{"files":[{"url":".\/.\/usdata\/ConnectingServoToComputer.jpg"}],"description":"Strip the corresponding wires and then screw them into the USB converter terminals that correspond.","components":[]}]}],"name":"USB to Motor Controller","license":"","notes":""},{"abstract":"","id":"1922376863","functions":[{"id":"728556721","description":"","implementations":[{"id":"766408515","quantity":1,"type":"part"},{"id":"173881220","quantity":2,"type":"part"},{"id":"190308674","quantity":1,"type":"part"},{"id":"1965925578","quantity":2,"type":"part"},{"id":"116116643","quantity":1,"type":"part"},{"id":"11083604","quantity":1,"type":"part"},{"id":"522428571","quantity":1,"type":"part"},{"id":"588964909","quantity":1,"type":"part"},{"id":"2073946119","quantity":1,"type":"part"},{"id":"535711406","quantity":1,"type":"part"},{"id":"392906382","quantity":2,"type":"part"},{"id":"2093352553","quantity":2,"type":"part"}]}],"authors":[],"files":[],"long_description":"The first prototype that was used to maintain a stable control over the PRO-1600RGB laser from Laserworld. This prototype is what was used to do primary testing and proof of this system as integrated into uManager microscopy setup software. It, however, implements an erroneous reading of the ILDA standard and as such is not guaranteed to work with all ILDA IO pins.\n\nAs such, this alpha version stands as proof of control of the PRO-1600RGB and may be tested against other ILDA laser boxes if so desired to ensure performance.","instructions":[{"name":"assembly","steps":[{"files":[{"url":".\/.\/usdata\/Breadboard Picture.png"}],"description":"See wiring diagram and schematics at https:\/\/github.com\/HopeCollegeSuperresolutionMicroscope\/CustomElectricalComponents\/tree\/master\/USB_TO_ILDA_ADAPTER","components":[]}]}],"name":"USB to ILDA Adapter","license":"","notes":"Schematic:\n\n The schematic makes use of a Deprected switch (see schematic itself for details). This switch\nwill become a production chokepoint. Efforts to formalize and proof v1.0 move toward this.\n\nPCB:\n\n The alpha prototype exists in a breadboarded state in the setup this lab tested against. As such,there are no Gerber files at this moment. It is seen as a better use of time to work on proving the v1.0 PCB instead. The following version however will require a reworking of uManager Device Library code to accomodate an increase in IO if that is desired."},{"abstract":"","id":"219949952","functions":[{"id":"1602677369","description":"","implementations":[{"id":"1178746898","quantity":2,"type":"part"},{"id":"2076837982","quantity":1,"type":"part"}]}],"authors":[],"files":[],"long_description":"","instructions":[{"name":"assembly","steps":[{"files":[],"description":"Pre-Aligning the laser beam to be centered in the cage (Vertical): If using the exact same products as this lab, the laser height should already be nearly level with the center of the cage system that is assembled. If you examine the unpowered laser unit, you will see that the laser beam's angle is the result of tilting two mirrors. Consequently, the height at which the beam is aligned is dependent on how accurately these mirrors are placed. Since there is no guaranteed tolerance on this height, the purchase of spacers like RS1M and addition to the mount plate legs, may be in order. As a good estimation for this height, first align the laser mount plate to the assembled cage system. DO NOT plug in the laser. Manually inspect the mirror through the display glass to see if it is nearly vertically centered (you may need to remove the guard tube for this inspection). If there is a discrepancy, measure the approximate change in height needed and order spacers to reach that height. (Note: you may also need longer screws is a large enough difference is discovered).","components":[]},{"files":[],"description":"Pre-Aligning the laser beam to be centered in the cage (Horizontal): With NO POWER to the laser, ensure that the Laser mirror inside the unit is roughly centered hoziontally at the end of the cage system. Reattach the the guard tube to the plate against the laser unit and slide the ND filter into place at its other end. Ensure that the laser unit is flush against the cage system plate (without applying pressure to the cage itself, and that the ND filter is flush (without actually touching the guard tube).","components":[]},{"files":[],"description":"Achieving a Visible beam for laser alignment: Before turning on the laser unit, you MUST have the proper laser safety glasses and take appropriate precautions. In order to align the beam fully, visible observation of the beam's position is necessary, but strategies for this alignment should be approved by someone familiar with laser safety. The steps in this guide are meant to present a means for aligning the beam, but advice from other familiar with laser alignment may be warranted. At no point should you ever stare directly into a laser, nor should you ever have a high-powered beam running through the cage system without appropriate blocking measures in place. In the most ideal circumstance, a simple camera may be setup to allow for remote viewing and observation of beam position changes. With the laser configured in Micro-manager and plugged in, first set all laser power levels to 0, and the X and Y to 0 respectively. Ensure that the Neutral Density filter's most opaque section covers the end of the beam guard tube. Place the Cage Alignment Plate in the cage system following the ND filter so that it hangs with little vibration. Turn the Single Beam switch on and then turn on the laser. Slowly raise the power of the laser you would like to align (red in our case) in Micro-manager. From experimental data, the red laser begins to emit around 3V with significantly decreased power. When you have reached the potential \"on\" threshold, adjust the ND filter to see if there is any visible laser on the Cage Alignment Plate (or even visible as a retro-reflection on the ND filter glass). If there is still no laser, move back to the most opaque section and increment the laser power again slightly. Repeat this cycle until a faintly visible beam shows up on the target (remember, the goal is to have something that can be visibly aligned without being dangerous to the aligner so caution is tantamount. DO NOT assume that the lasing unit in your purchased unit will increase it's power at a similar rate as this lab's setup, and therefore always reset the ND filter to max opacity before slowly decreasing it to get a low powered beam).","components":[]},{"files":[],"description":"Powered Alignment of the laser (horizontal): Once a beam is visible on Cage Alignment Plate, verify that the vertical height of the beam is nearly aligned with the cage plate (remember that your height may vary by the height of a 1 mm spacer so close is good enough). If your laser height is off, (assuming your unit's mirrors were not bent), please determine the combination of spacers that would be necessary to adjust the mounting plate height. The unit should be unplugged and realigned accordingly. If the laser height is sufficient, carefully move the laser unit left and right so that its horizontal component is nearly centered. When this is done, securely clamp the laser mouniting plate to the Breadboard.","components":[]},{"files":[],"description":"Alignment of beam in beam-expander cage assembly: With the laser beam off again, place the Cage Alignment Plate near the kinematic mirror mount that points to the, now-fastened in-place, laser unit. Again, following the \"Achieving a Visible beam for laser alignment\" steps, ensure that a beam is visible on the target. You will now use the Dielectric mirror in the kinematic mirror mount, and the X and Y position controls in Micro-manager to align the beam so that it is centered for the length of the proceeding cage system. In order to ensure this, you will want to verify that the laser is centered on the Cage Alignment Plate, along the whole cage system after the kinematic mirror. As a general rule, if the Dielectric mirror tilts the beam down, then the laser beam will want to tilt the beam up; recall that, if you only move one mirror to center the beam at one location, when you move the target further along the cage, is will continue at the single angle. Note: Do not have the Beam Expander Lenses in during this alignment phase.","components":[]},{"files":[],"description":"Alignment of Beam Expander Centers: The two lenses that are placed in the Beam Expander line, are added to kinematic mounts. This means the lenses can adjust their horizontal and vertical position, and consequently the centerline of the now centered laser. In order to ensure that we do not alter the previously centered laser line, you will now want to add the lenses to their respective mounts. Once mounted, you will want to get a laser beam by \"Achieving a Visible beam for laser alignment\". Placing the Cage Alignment Plate in front of the first lens, move it to different positions along the cage rods and ensure that the beam is centered; the beam will expand and shrink as the lens is causing it to focus. If the beam is not centered, adjust the knobs on the kinematic mount to move the beam to center. Once the first lens is centered, you will want to follow suit with the second lens. Please note, the lens distances are not yet confirmed, but their center line is (this may fall out of focus in the future, but can be adjusted by just following this step).","components":[]},{"files":[],"description":"Pre-alignment of Camera: After the laser beam is aligned along the beam expander portion of the cage assembly, again turn off the laser. You will then want to rotate the Dichroic mirror so that is it reflecting light down toward the camera line (NOTE: the Camera Line should not be installed at this point). If you have added a bandpass filter, remove it as well. \n\nEnsuring that the light is arriving at 45 degrees: Remove the dust-cap off the end of the Dichroic Filter Cage and add 2 ER8 rods to the end. Add the Cage Alignment Plate to the rods. You will then want to follow the steps to \"Achieving a Visible beam for laser alignment\". If may be necessary to increase the intensity of the beam more (we recommend by slightly lowering the ND filter), until a visible beam is apparent on the Cage Alignment Plate. In order to verify that the dichroic mirror is indeed pointing down at a 45 degree angle, rotate the mirror slightly to place the beam centered on the target.\n\nSetting up Beam Expander for focal plane: Using the Cage Alignment Plate still, you will then want to move the second lens either closer or farther from the first so that the size of the beam on the Cage Alignment Plate does not change along the length of the ER8 cage rod added. This ensures that we have a more observable sized spot for detecting the focal point, that is also still collimated light.\n\nEnsuring Camera Line Mirror alignment: Once the light is ensured at 45 degrees down into the camera line, turn off the laser and switch the ER8 rods to the base of the Kinetic Mirror Mount on the camera line. Add the Cage Alignment Plate onto the rods. You will again want to get a laser beam as described in \"Achieving a Visible beam for laser alignment\". With the beam showing on the target, adjust the Kinematic Mirror so that the the laser beam is centered on the Cage Alignment Plate. Verify that the laser stays nearly centered along the whole length of the ER8 rod. Please Note: you are passing the laser light through a lens, so you should expect the size of the beam to change along the length of the ER8; the center should remain constant though. \n\n Finding the focal plane: \nWith the beam centered, you will now want to move the Cage Alignment Plate along the length of the ER8 rod to the point that the beam is a single point (goes through the hole). This is the focal point of the beam and consequently the image from the objective. Mark that point on the ER8 rod.","components":[]},{"files":[],"description":"Camera Placement at Focal Plane: Caution: The laser should not be on during this. Additionally, before adding the Camera to the Camera Line, rotate the Dichroic mirror so that the laser is directed toward the objective and stage.\n\n In order to place the Camera Sensor at the focal plane, you will want to take stock of the depth at which the sensor sits, (this lab measured the depth, but then found that verification by eyeball was enough). Using two people, go ahead and attach the lens tubes to the Kinematic mirror mount, making sure to keep it from extending into where the camera needs to be. A second person will then slide the camera into place and align its sensor plane visually with the mark on the ER8 rod (keeping the base post loose to raise and lower it). The first person will then extend the lens tube until it is bumping the face of the camera. Once the tube is extended, remove the ER8 rods and raise the camera to the height of the lens tube. With one person holding the camera steady, slowly thread the tube and adapter into the the camera (being sure to let the tube slide in, rather than the camera move forward. (Caution: Do Not force the tube to turn when starting, you do not want to strip the threads, go slowly and adjust the height\/angle of the camera to make sure the hole aligns with the tube). When the camera is attached to the lens tube, tighten the post nut at the correct height and then clamp the camera to the breadboard in its current place.","components":[]},{"files":[],"description":"Realigning the Dichroic mirror: Now that the camera has been placed in line, add the bandpass filter for the given laser as a precaution. Then follow the directions for \"Ensuring the light is arriving at 45 degrees\", only with the objective of aligning the mirror to reflect up toward the stage now.","components":[]},{"files":[],"description":"Beam Expander Distance: To achieve even illumination across the sample, the beam expander placement may need to be adjusted. Using proper laser safety practices, slide the beam expander until an even illumination is achieved.","components":[]}]}],"name":"Calibration Steps for Optics and Alignment","license":"","notes":""}],"parts":[{"id":"1854461583","files":[],"description":"Red-green-blue entertainment laser unit.","name":"Laser","manufacturing_instruction":{"steps":[]},"supplier_part_num":"PRO-1600RGB","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.laserworld.com\/shop\/laserworld-lasers\/proline-series\/laserworld-pro-1600rgb","supplier":"LaserWorld"},{"id":"42248522","files":[{"url":".\/.\/usdata\/RMS100X-PFO-AutoCADPDF-2.png"}],"description":"Plan Fluorite Oil Immersion Objective, 1.30 NA, 0.20 mm WD","name":"100x Objective","manufacturing_instruction":{"steps":[]},"supplier_part_num":"RMS100X-PFO","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=RMS100X-PFO","supplier":"Thorlabs"},{"id":"1273959861","files":[],"description":"","name":"Immersion Oil for Objective","manufacturing_instruction":{"steps":[]},"supplier_part_num":"MOIL-30","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=MOIL-30","supplier":"Thorlabs"},{"id":"1181552474","files":[{"url":".\/.\/usdata\/B3048F-AutoCADPDF.png"}],"description":"30\" x 48\" x 2.4\", 1\/4\"-20 Mounting Holes","name":"Breadboard, Nexus","manufacturing_instruction":{"steps":[]},"supplier_part_num":"B3048F","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=B3048F","supplier":"Thorlabs"},{"id":"31738501","files":[],"description":"CCD camera with 2.8 MegaPixels","name":"Camera","manufacturing_instruction":{"steps":[]},"supplier_part_num":"","material_amount":"","manufacturer_part_num":"Retiga R3","material_unit":"NONE","url":"https:\/\/www.qimaging.com\/products\/cameras\/scientific\/retiga-r3.php","supplier":"Mager Scientific"},{"id":"245102677","files":[{"url":".\/.\/usdata\/AC254-200-A-ML-AutoCADPDF.png"}],"description":"","name":"Lens f=200 mm, 1\" Achromatic Doublet, SM1-Threaded Mount, ARC: 400-700 nm","manufacturing_instruction":{"steps":[]},"supplier_part_num":"AC254-200-A-ML","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=AC254-200-A-ML","supplier":"Thorlabs"},{"id":"1675867349","files":[{"url":".\/.\/usdata\/AC254-030-A-ML-AutoCADPDF.png"}],"description":"","name":"Lens f=30 mm, 1\" Achromatic Doublet, SM1-Threaded Mount, ARC: 400-700 nm","manufacturing_instruction":{"steps":[]},"supplier_part_num":"AC254-030-A-ML","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=AC254-030-A-ML","supplier":"Thorlabs"},{"id":"93878551","files":[{"url":".\/.\/usdata\/AC254-100-A-ML-AutoCADPDF.png"}],"description":"","name":"Lens f=100 mm, 1\" Achromatic Doublet, SM1-Threaded Mount, ARC: 400-700 nm","manufacturing_instruction":{"steps":[]},"supplier_part_num":"AC254-100-A-ML","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=AC254-100-A-ML","supplier":"Thorlabs"},{"id":"214211596","files":[{"url":".\/.\/usdata\/SemrockFilterDetails.png"}],"description":"Dual-edge standard epi-fluorescence dichroic beamsplitter","name":"Dichroic beamsplitter 545\/640 nm","manufacturing_instruction":{"steps":[]},"supplier_part_num":"FF545\/650-Di01-25x36","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.semrock.com\/filterdetails.aspx?id=ff545\/650-di01-25x36","supplier":"Semrock"},{"id":"1549084167","files":[],"description":"","name":"Bandpass filter red, 25mm (700\/75)","manufacturing_instruction":{"steps":[]},"supplier_part_num":"ET700\/75m","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.chroma.com\/products\/parts\/et700-75m","supplier":"Chroma"},{"id":"483424046","files":[{"url":".\/.\/usdata\/SemrockFilterDetails582.png"}],"description":"582\/75 nm single-band bandpass filter, 25 mm x 5.0 mm","name":"Bandpass filter green, 25mm (582\/75)","manufacturing_instruction":{"steps":[]},"supplier_part_num":"FF01-582\/75-25","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.semrock.com\/filterdetails.aspx?id=ff01-582\/75-25","supplier":"Semrock"},{"id":"1663798749","files":[{"url":".\/.\/usdata\/RS38_M-AutoCADPDF.png"}],"description":"RS38\/M - 25.0 mm Pillar Post, M6 Taps, L = 38 mm, M4 Adapter Included","name":"25mm Post, (38 mm height*)","manufacturing_instruction":{"steps":[]},"supplier_part_num":"RS38\/M","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=RS38\/M","supplier":"Thorlabs"},{"id":"1970249459","files":[{"url":".\/.\/usdata\/BE1_M-AutoCADPDF.png"}],"description":"For clamping to optical breadboard.","name":"31.8 mm Studded Pedestal Base Adapter, M6 Thread","manufacturing_instruction":{"steps":[]},"supplier_part_num":"BE1\/M","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=BE1\/M#ad-image-0","supplier":"Thorlabs"},{"id":"1651425089","files":[{"url":".\/.\/usdata\/CF125-AutoCADPDF.png"}],"description":"For adjustable positioning of platform on board.","name":"Short Clamping Fork, 1.24\" Counterbored Slot, Universal","manufacturing_instruction":{"steps":[]},"supplier_part_num":"CF125","material_amount":"","manufacturer_part_num":"","material_unit":"NONE","url":"https:\/\/www.thorlabs.com\/thorproduct.cfm?partnumber=CF125#ad-image-0","supplier":"Thorlabs"},{"id":"1279133013","files":[{"url":".\/.\/usdata\/RS5M-AutoCADPDF.png"}],"description":"25 mm Post Spacer, Thickness = 5 mm. \nDue to the uncertainty of height of the raster mirrors in the laser, it may be necessary to add additional height to the Optics Posts and screws holding them. 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