diSPIM Wiki software

software:fiji_mvr

anonymous@undisclosed.example.com (Anonymous) — Sat, 27 Jul 2019 18:19:52 +0000

Fiji MVR (Multiview Reconstruction) This software is for registering and fusing the datasets from two views. It was originally developed for OpenSPIM-like setups but works well for diSPIM data as well. See homepage at . As of April 2015 the MVR plugin allows for direct importing of Micro-Manager datasets. Previously the Micro-Manager plugin's export function was used (it is still required for

software:gpu_dispimfusion

anonymous@undisclosed.example.com (Anonymous) — Mon, 04 Nov 2024 18:36:10 +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:imagej_macro

anonymous@undisclosed.example.com (Anonymous) — Thu, 08 Aug 2019 20:56:47 +0000

Imagej Macro *Deprecated: Please see diSPIM Preprocessing* Min Guo, Yicong Wu, and Hari Shroff, February 2016 Tutorial for using the image shifting macro, for diSPIM data acquired in stage-scanning mode The image shifting macro preprocesses diSPIM data acquired in stage-scanning mode before further analysis (e.g. deconvolution, segmentation etc.). The macro offers background subtraction, image shifting and automated region of interest detection in a graphical user interface for easy user in…

software:labview

anonymous@undisclosed.example.com (Anonymous) — Sun, 14 Feb 2016 13:41:33 +0000

Labview LabView implementations have been created by the Hari Shroff lab and used by collaborators. Contact them directly for LabView code (also available on wormguides.org)., In general LabView is recommended only for groups doing significant custom software development within an existing LabView framework. End users are probably better off using Micro-Manager or a commercial software. Micro-manager is open-source and extensible so it can also be utilized by groups doing custom software d…

software:micro-manager

anonymous@undisclosed.example.com (Anonymous) — 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

software:mipav_generatefusion

anonymous@undisclosed.example.com (Anonymous) — Sat, 20 Apr 2019 00:36:27 +0000

MIPAV Generatefusion MIPAV is a framework not unlike Fiji, and the generatefusion plugin was developed in collaboration with the Shroff lab. It does intensity-based registration and joint deconvolution. You can download MIPAV at and then install the plugin. As of early 2019 this is still the cannonical workflow for some groups, though the Shroff lab has been developing a successor software.

software:momomagick

anonymous@undisclosed.example.com (Anonymous) — Tue, 20 Aug 2024 23:22:19 +0000

momomagick (& momotrack) momomagick is a Python toolbox to register, deconvolve and fuse diSPIM images from the command-line interface. Min Guo originally implemented the registration algorithm used in this toolbox. By using Python, scripts in this toolbox can utilize various registration methods, such as Phase-only correlation (POC) and brute-force matching, employing various optimization algorithms provided by Scipy. Scripts can run on nVidia GPUs through cupy/cuda libraries. This toolbox was…

software:start

anonymous@undisclosed.example.com (Anonymous) — Tue, 20 Aug 2024 17:02:52 +0000

Software The first step is acquiring the image data, then the images must be manipulated to give the information the experimenter needs. Data acquisition can be performed using the ASIdiSPIM plugin in Micro-Manager, using custom-written LabView programs, or using other software that is not yet documented on this wiki (both commercial or home-built). The acquisition software will produce image files.software index