Journal Article

DZNE-2026-00807

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png MotilA – A Python pipeline for the analysis of microglial fine process motility in 3D time-lapse multiphoton microscopy data

Musacchio, F. (First author)DZNE* ; Crux, S.DZNE* ; Nebeling, F.DZNE* ; Gockel, N.DZNE* ; Fuhrmann, F.DZNE* ; Fuhrmann, M. (Last author)DZNE*

2025

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Please use a persistent id in citations: doi:10.21105/joss.09267

Abstract: MotilA is an open-source Python pipeline for quantifying microglial fine-process motility in4D (TZYX) or 5D (TZCYX) time-lapse fluorescence microscopy data, supporting both singlechannel and two-channel acquisition. It was developed for high-resolution in vivo multiphotonimaging and supports both single-stack and cohort-scale batch analyses. The workflowperforms sub-volume extraction, optional registration and spectral unmixing, a maximumintensity projection along the Z-axis, segmentation, and pixel-wise change detection to computethe turnover rate (TOR). MotilA specifically targets pixel-level process motility rather thanobject tracking or full morphometry. The code is platform independent, documented withtutorials and example datasets, and released under GPL-3.0.

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Contributing Institute(s):

1. Neuroimmunology and Imaging (AG Fuhrmann)

Research Program(s):

1. 352 - Disease Mechanisms (POF4-352) (POF4-352)

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Database coverage:
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Linked articles:

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Journal Article Gockel, N. (First author)DZNE* ; Nieves-Rivera, N. ; Druart, M. ; Jaako, K. ; Fuhrmann, F.DZNE* ; Musacchio, F.DZNE* ; Antony, H.DZNE* ; Mittag, M.DZNE* ; Crux, S.DZNE* ; Poll, S.DZNE* ; Jansone, B. ; Fuhrmann, M.DZNE* ; Le Magueresse, C.
Schizophrenia-associated complement C4 impairs synaptic connectivity and decreases microglia-synapse interactions through CR3 signaling.
Cell reports 45(4), 117161 (2026) [10.1016/j.celrep.2026.117161]2026   Files BibTeX | EndNote: XML, Text | RIS

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Software Musacchio, F.DZNE* ; Crux, S.DZNE* ; Nebeling, F.DZNE* ; Gockel, N. E.DZNE* ; Fuhrmann, F.DZNE* ; Fuhrmann, M.DZNE*
Software: MotilA – A Python pipeline for the analysis of microglial fine process motility in 3D time-lapse multiphoton microscopy data, v1.1.0
Zenodo (2025) [10.5281/zenodo.17807127]2025 BibTeX | EndNote: XML, Text | RIS

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