Importing Imaris files using import 3D tool

Managing anatomically complex model cells with the CellBuilder. Importing morphometric data with NEURON's Import3D tool or Robert Cannon's CVAPP. Where to find detailed morphometric data.
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mehaj
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Importing Imaris files using import 3D tool

Post by mehaj »

Hello everyone,

I have traced morphologies of neurons using Oxford Imaris software. I can only export them as Imaris files or TIF and not as SWC. Is there a way to import the Imaris files directly into the import 3d tool of NEURON? I tried to look for a way to convert the Imaris files to SWC but could not find any good options.

I would really appreciate if you could suggest any ways to import these files directly or to convert them to an acceptable format.

Thanks!

Meha
ted
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Re: Importing Imaris files using import 3D tool

Post by ted »

I tried to look for a way to convert the Imaris files to SWC but could not find any good options.
Import3d's algorithms require an input file that contains morphometric data, specifically measurements of diameters at particular locations in space, structured in a way that identifies neurites and branch points. According to
https://imaris.oxinst.com/support/imaris-file-format
the Imaris file format is basically a multiresolution image format. Converting image data to morphometric data is not an easy task. There is third-party software to make the task easier, some commercial and some available at no charge (e.g. Vaa3D), but you'll have to discover if any of it can deal with IMS files.
mehaj
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Joined: Fri Sep 10, 2021 2:25 am

Re: Importing Imaris files using import 3D tool

Post by mehaj »

Thank you, Ted. This was very helpful!
ted
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Re: Importing Imaris files using import 3D tool

Post by ted »

This article mentions several approaches to semiautomatic morphological construction, and contains
a detailed, step-by-step description of a workflow for semiautomatic morphological reconstruction (using freely available software developed in our laboratory)
:

@InCollection{WOS:000635353100010,
author = {Hartveit, Espen and Zandt, Bas-Jan and Veruki, Margaret Lin},
title = {{Multiphoton Excitation Microscopy for the Reconstruction and Analysis of Single Neuron Morphology}},
booktitle = {{MULTIPHOTON MICROSCOPY}},
year = {{2019}},
editor = {{Hartveit, E}},
volume = {{148}},
series = {{Neuromethods}},
pages = {{161-194}},
abstract = {{Neurons are the main cellular components of the circuits of the central
nervous system (CNS). The dendritic and axonal morphology of individual
neurons display marked variability between neurons in different regions
of the CNS, and there is evidence that the morphology of a neuron has a
strong impact on its function. For studies of structure-function
relationships of specific types of neurons, it is important to visualize
and quantify the complete neuronal morphology. In addition, realistic
and detailed morphological reconstruction is essential for developing
compartmental models that can be used for studying neuronal computation
and signal processing. Here we describe in detail how multiphoton
excitation (MPE) microscopy of dye-filled neurons can be used for
visualization and imaging of neuronal morphology, followed by a workflow
with digital deconvolution and manual or semiautomatic morphological
reconstruction. The specific advantages of MPE structural imaging are
low phototoxicity, the ease with which it can be combined with parallel
physiological measurements from the same neurons, and the elimination of
tissue post-processing and fixation-related artifacts. Because manual
morphological reconstruction can be very time-consuming, this chapter
also includes a detailed, step-by-step description of a workflow for
semiautomatic morphological reconstruction (using freely available
software developed in our laboratory), exemplified by reconstruction of
a retinal amacrine cell (AII).}},
doi = {10.1007/978-1-4939-9702-2_8},
}
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