| descSPIM.basic.230502 | Notes | Part.Number | Quantity |
|---|---|---|---|
| Det. Optics | CMOS camera ＊1 | CS895MU | 1 |
| Adapter with External C-Mount Threads and Internal SM1 Threads | SM1A9 | 1 | |
| SM1 Lens Tube, 1.00" Thread Depth, One Retaining Ring Included | SM1L10 | 1 | |
| SM1 Lens Tube, 0.30" Thread Depth, One Retaining Ring Included | SM1L03 | 1 | |
| Adapter with External SM1 Threads and Internal SM2 Threads | SM1A2 | 2 | |
| Tube Lens, f = 100 mm, ARC: 350 - 700 nm, External SM2 Threads ＊2 | TTL100-A | 1 | |
| SM1 Lens Tube, 1.50" Thread Depth, One Retaining Ring Included | SM1L15 | 1 | |
| Fast-Change, SM1 Lens Tube Filter Holder for Filters 3.5 - 6.3 mm Thick ＊3 | SM1QP | 1 | |
| Extra Filter Carriage for Filters 3.5 - 6.3 mm Thick ＊3 | SM1QT | 1 | |
| Premium Bandpass Filter, Ø25 mm, CWL = 520 nm, FWHM = 40 nm ＊4 | FBH520-40 | 1 | |
| Premium Bandpass Filter, Ø25 mm, CWL = 550 nm, FWHM = 40 nm ＊4 | FBH550-40 | 1 | |
| Premium Bandpass Filter, Ø25 mm, CWL = 600 nm, FWHM = 40 nm ＊4 | FBH600-40 | 1 | |
| Premium Bandpass Filter, Ø25 mm, CWL = 700 nm, FWHM = 40 nm ＊4 | FBH700-40 | 1 | |
| Ø25.0 mm Longpass Filter, Cut-On Wavelength: 550 nm | FBLF0550 | 1 | |
| SM1 Lens Tube Without External Threads, 1/2" Long, Two Retaining Rings Included | SM1M05 | 1 | |
| Adapter with External SM1 Threads and Internal M25 x 0.75 Threads | SM1A12 | 1 | |
| 2X obj lens (NA 0.1, w.d. 56.3 mm) | TL2X-SAP | 1 | |
| Clamp for SM1 Lens Tubes and C-Mount Extension Tubes | SM1TC | 2 | |
| Ø12.7 mm Post Holder, Spring-Loaded Hex-Locking Thumbscrew, L=30 mm | PH30/M | 2 | |
| Ø12 mm Optical Post, SS, M4 Setscrew, M6 Tap, L = 30 mm | TR30/M-JP | 2 | |
| 25 mm Travel Linear Translation Stage, Side-Mounted Micrometer, M6 x 1.0 Taps | XR25P/M | 1 | |
| 25 mm Motorized Actuator with Ø3/8" Barrel (0.5 m Cable) | Z825B | 1 | |
| K-Cube Brushed DC Servo Motor Controller (Power Supply Not Included) | KDC101 | 1 | |
| K-Cube Power Supply, 15V 2.4A, Japan | KPS201 | 1 | |
| NA | |||
| Sample holder | 150mm Long Rail for XR25 | XR25DR2 | 1 |
| Metric Linear Translation Platform, 25mm | XR25P/M | 2 | |
| 25 mm Motorized Actuator with Ø3/8" Barrel (0.5 m Cable) | Z825B | 1 | |
| K-Cube Brushed DC Servo Motor Controller (Power Supply Not Included) | KDC101 | 1 | |
| K-Cube Power Supply, 15V 2.4A, Japan | KPS201 | 1 | |
| Mounting Post Base 2.48 x 0.4 x 0.265 | PB1 | 1 | |
| 38mm Solid Post 50mm Length | P50/M | 1 | |
| Metric Coarse Adjustable Height Platform | C1519/M | 1 | |
| 13mm Travel Manual Vertical Stage | MVS05/M | 1 | |
| Dovetail Optical Rail, 300 mm, Metric | RLA300/M | 2 | |
| High-Precision Rotation Stage, M6 and M4 Taps | PR01/M | 1 | |
| Cage Assembly Rod, 2" Long, Ø6 mm, 4 Pack | ER2-P4 | 1 | |
| Cage Assembly Rod, 4" Long, Ø6 mm, 4 Pack | ER4-P4 | 1 | |
| Compact Cage Assembly Rod, 1.5" Long, Ø4 mm, 4 Pack | SR1.5-P4 | 1 | |
| Blank 30 mm Cage Plate, 8.9 mm Thick, M4 x 0.7 Tap | CP31/M | 1 | |
| Blank 16 mm Cage Plate, 0.25" Thick, 4-40 and M3 Taps | SP01 | 1 | |
| 30 mm to 16 mm Cage Adapter Plate, M4 Tap | SP15/M | 1 | |
| NA | |||
| Ex. Optics | Metric Threaded Cage Plate | CP33/M | 3 |
| SM1 to FC/APC Fiber Bulkhead Adapter ＊5 | SM1FCA | 1 | |
| High Precision Translating Lens Mount for 1" Optics | CXY1A | 1 | |
| f = 100 mm, Ø1" Achromatic Doublet, ARC: 400 - 700 nm | AC254-100-A | 1 | |
| Metric SM1 Right Angle Kinematic Mirror Mount | KCB1EC/M | 3 | |
| 1" Broadband Dielectric Elliptical Mirror, 400 - 750 nm | BBE1-E02 | 3 | |
| Ø1" Adjustable Lens Tube, 0.31" Travel Range | SM1V05 | 2 | |
| SM1 Lens Tube, 1.00" Thread Depth, One Retaining Ring Included | SM1L10 | 1 | |
| 13 mm manual Translation stage, 30 mm Cage Compatible | CT1A/M | 1 | |
| f = 500.0 mm, Ø1", N-BK7 Mounted Plano-Convex Round Cyl Lens, ARC 350-700 | LJ1144RM-A | 1 | |
| f = 150.0 mm, Ø1" Cylindrical Achromat, AR Coating: 350 - 700 nm | ACY254-150-A | 1 | |
| Ø12.7 mm Post Holder, Spring-Loaded Hex-Locking Thumbscrew, L=150 mm | PH150/M | 3 | |
| Ø12.7 mm Post Holder, Spring-Loaded Hex-Locking Thumbscrew, L=50 mm | PH50/M | 1 | |
| Ø12 mm Optical Post, SS, M4 Setscrew, M6 Tap, L = 50 mm | TR50/M-JP | 4 | |
| Cage Assembly Rod, 4" Long, Ø6 mm, 4 Pack | ER4-P4 | 4 | |
| Cage Assembly Rod, 2" Long, Ø6 mm, 4 Pack | ER2-P4 | 2 | |
| Cage Assembly Rod, 3" Long, Ø6 mm, 4 Pack | ER3-P4 | 1 | |
| Snap-On 30 mm Cage Mounting Bracket, #8 (M4) Slot | CPMA3 | 4 | |
| NA | |||
| Others | Aluminum Breadboard, 300 mm x 450 mm x 12.7 mm, M6 Taps | MB3045/M | 1 |
| Magnetic Laser Safety Screen, 200 mm x 75 mm, Metric Engraving | TPSM1/M | 1 | |
| 30 mm Cage Alignment Plate with Ø5 mm Hole | CPA2 | 1 | |
| 15-Piece Balldriver and Hex Key Kit with Stand, Metric | TC3/M | 1 | |
| M6 x 1.0 Stainless Steel Cap Screw, 10 mm Long, 25 Pack | SH6MS10 | 2 | |
| M4 x 0.7 Stainless Steel Cap Screw, 6 mm Long, 50 Pack | SH4MS06 | 1 | |
| M6 x 1.0 Stainless Steel Setscrew, 10 mm Long, 25 Pack | SS6MS10 | 1 | |
| M6 x 1.0 Stainless Steel Nut, 50 Pack | N6MS010 | 1 | |
| NA | |||
| Besides Thorlabs | Multi-line laser ligh source (Cobolt skyra etc.) ＊6 | NA | |
| Multi-line laser ligh source (Coherent OBIS, Cobolt 06 series etc.) ＊6 | NA | ||
| M6 cap screw (60 mm-length) | e.g. TRUSCO PRO TOOL B44-0660 | 4 | |
| 4-side cleared BK7 cuvette (Opt. Length 10 mm or 20 mm; GL Science etc) | F10-G-10 or F10-G-20 (GL Science) | NA | |
| 4-side cleared disposable cuvette (Opt. Length 10 mm; Thermo Fisher Scientific, Bio-Rad etc) | 14-955-129 (Thermo Fischer) 1702415 (Bio-Rad) | NA | |
| NA | |||
| NA | |||
| ＊1 Other monochro cameras (Thorlabs or others) are acceptable accoding to desired FOV | NA | ||
| ＊2 The tube lens of 200 mm focal length with additional SM1L35 can be set for 2X magnification. | NA | ||
| ＊3 If you use the filter wheel (LTFW6; 50,755 JPY), SM1M05 should be exchange to SM1L05. | NA | ||
| ＊4-1 Filters should be selected by users | NA | ||
| ＊4−2 Filter holder is designed for >3.5 mm thickness. If thinner, SM1QU/SM1QTU can be used. | NA | ||
| ＊5 If FC/PC fiber, SM1FC can be used. | NA | ||
| ＊6 Sigle-mode fiber coupled laser light source | NA | ||
| Provided by Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University. All Rights Reserved. | NA |
Software
Flat-field correction (ImageJ macro)
Not available anymore (404 error)
How to use:
- prepare a reference xy image(1) and a sample xyz stack(2).
- a reference xy image In order to get the reference image, hogehoge… acquired using dye-solving solution (e.g., CUBIC-R + FITC reagent)…
- a sample xyz image stack to be corrected
- run macro with ImageJ/Fiji
Tiling light-sheet method: tiling x position finder (ImageJ macro)
Not available (404 error)
Compile NIfTI file from TIF(TIFF) stacks: .ipynb file
:warning: Note: This code has been tested only on Ubuntu. While it may work on other operating systems, compatibility and functionality are not guaranteed.
Preparations:
Install ImageMagick
Install C3D
How to use: Please follow the instructions in the code.
Stitching with Bigstitcher
Under review…
0-180 digree fusion by 3D slicer and Bigstitcher
Under review…
descSpim parts list
(Change table display see Tables (how to display in R/Q Notes))