diSPIM Wiki

media:publications - [Biology-Focused]

jond@undisclosed.example.com (Jon Daniels) — Sat, 21 Feb 2026 00:29:32 +0000

Publications Microscopy-Focused * Airy light-sheet Raman imaging. Optics Express 29, 31941-31951 (2021). doi: 10.1364/OE.435293. PMID: 34615275 * used ASI scanner and custom ASI XYZ stage on inverted microscope * Reflective imaging improves spatiotemporal resolution and collection efficiency in light sheet microscopy. Nat. Comm. 8:1452 (Nov 2017). doi: 10.1038/s41467-017-01250-8. PMID: 29129912 * iSPIM/diSPIM on reflective substrate for 2/4 simultaneous views

docs:deskew - ["Deskewing" (Reslicing) in Micro-Manager 2.0 Image Processor]

jond@undisclosed.example.com (Jon Daniels) — Tue, 02 Dec 2025 21:56:25 +0000

Deskewing This page is an overview of deskewing. Image viewers such as FIJI assume that stacks of camera images are formed using motion orthogonal to the image plane, but that assumption is not true for single-objective light sheet, lattice light sheet, and diSPIM with stage scanning.

docs:mm_dispim_plugin_user_guide - [Overview Acquisition]

jond@undisclosed.example.com (Jon Daniels) — Tue, 20 May 2025 17:18:48 +0000

Micro-Manager diSPIM Plugin User Guide The diSPIM plugin adds functionality to Micro-Manager from alignment to acquisition. This user guide gives an introduction to the utility of each of the tabbed panels in the plugin, as well as guidance on hardware- and sample-based considerations.

software:micro-manager - [Micro-manager diSPIM Plugin]

jond@undisclosed.example.com (Jon Daniels) — Wed, 14 May 2025 21:04:43 +0000

Micro-manager diSPIM Plugin There is a Micro-manager plugin to control the diSPIM. It is part of the standard Micro-Manager build under Plugins -> Device Control -> ASIdiSPIM. Details about the plugin operation can be found in the manual section of this website in the

hardware:objectives - [Mechanical Angle]

jond@undisclosed.example.com (Jon Daniels) — Mon, 31 Mar 2025 15:23:06 +0000

Objectives The choice of light sheet objectives is limited because they must be co-focused without bumping into each other. See more details below on this page in the section Mechanical angle. The most commonly-used objectives for (symmetric) diSPIM are 40x water-dipping objectives with a NA of 0.8 (Nikon CFI Apo 40XW NIR). Other possibilities include the Olympus 20x/0.5 water (UMPLFLN20XW)

hardware:controller - [Required software and instructions]

jond@undisclosed.example.com (Jon Daniels) — Fri, 21 Mar 2025 18:14:03 +0000

Controller The diSPIM uses ASI's modular controller, the TG-1000 or “Tiger” controller. It has separate cards for controlling the XY stage, linear stages, micro-mirrors (scanners), triggering cameras/lasers, driving piezo objective movers if present, driving filterwheels if present, etc.

software:gpu_dispimfusion

jond@undisclosed.example.com (Jon Daniels) — Mon, 04 Nov 2024 18:35:56 +0000

diSPIM preprocessing & GPU diSPIMFusion To obtain a 3D image with isotropic resolution, diSPIM images typically require preprocessing before fusion. An ImageJ macro with a straight-forward user interface, is provided for each purpose. Preprocessing involves background subtraction, region of interest (ROI) cropping, and 3D orientation; additionally, stage-scanning acquisitions must undergo

software:cartoons_mainwindow.jpg - created

tmiyoshi@undisclosed.example.com (Takushi Miyoshi) — Tue, 20 Aug 2024 17:07:55 +0000

docs:um-dataanalyis-tab.png - created

jond@undisclosed.example.com (Jon Daniels) — Mon, 20 May 2024 15:51:01 +0000

docs:deskew_from_lamb_paper.png - created

jond@undisclosed.example.com (Jon Daniels) — Mon, 20 May 2024 15:42:18 +0000

hardware:oly20x_thor20x.pdf - created

jond@undisclosed.example.com (Jon Daniels) — Tue, 08 Aug 2023 22:37:19 +0000

hardware:config11_57-12-19_qty_2.pdf - created

jond@undisclosed.example.com (Jon Daniels) — Wed, 26 Apr 2023 18:13:27 +0000

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brandon@undisclosed.example.com (Brandon Simpson) — Thu, 18 Nov 2021 18:39:25 +0000

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brandon@undisclosed.example.com (Brandon Simpson) — Thu, 18 Nov 2021 18:29:56 +0000

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tokaihit@undisclosed.example.com (Tokai Hit Co. Ltd) — Thu, 19 Nov 2020 08:02:28 +0000

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tokaihit@undisclosed.example.com (Tokai Hit Co. Ltd) — Thu, 19 Nov 2020 08:01:08 +0000

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tokaihit@undisclosed.example.com (Tokai Hit Co. Ltd) — Thu, 19 Nov 2020 05:41:19 +0000

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tokaihit@undisclosed.example.com (Tokai Hit Co. Ltd) — Thu, 19 Nov 2020 05:41:12 +0000

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tokaihit@undisclosed.example.com (Tokai Hit Co. Ltd) — Thu, 19 Nov 2020 04:32:12 +0000

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tokaihit@undisclosed.example.com (Tokai Hit Co. Ltd) — Thu, 19 Nov 2020 04:09:12 +0000