Apr 23, 2026

MANUAL CELL COUNTING of FISH-LABELED CELLS - ORAMACELL PROTOCOL V.2

DOI
https://dx.doi.org/10.17504/protocols.io.e6nvwqy87vmk/v2
  • 1Oramacell, Paris, France;
  • 2Sorbonne Université, CNRS, Inserm, Institut de Biologie Paris Seine (IBPS), Centre de Neuroscience Sorbonne Université (NeuroSU), 75005, Paris, France;
  • 3Laboratory of Cholinergic Signaling, Institute of Physiology of the Czech Academy of Sciences, Prague, 14200, Czech Republic;
  • 4Lund University, Dept Experimental Medical Science, Molecular Neuroanatomy Lab, Biomedical Centre, 221 84 Lund, Sweden
  • Lund University
Åsa Wallén-Mackenzie
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DOI: https://dx.doi.org/10.17504/protocols.io.e6nvwqy87vmk/v2
Protocol Citation: Sylvie Dumas, Véronique Bernard, Alice Abbondanza, Åsa Wallén-Mackenzie 2026. MANUAL CELL COUNTING of FISH-LABELED CELLS - ORAMACELL PROTOCOL. protocols.io https://dx.doi.org/10.17504/protocols.io.e6nvwqy87vmk/v2Version created by Åsa Wallén-Mackenzie
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 22, 2026
Last Modified: April 23, 2026
Protocol  Integer ID: 315497
Keywords: ASAPCRN, cell, oramacell protocol manual cell counting of fish, oramacell protocol manual cell counting, labeled cell, fish protocol, fish protocol in separate link, fish
Funders Acknowledgements:
ASAP
Grant ID: ASAP-025188
Abstract
MANUAL CELL COUNTING of FISH-labeled cells
(FISH protocol in separate link)
Cell countings for quantification can be performed manually using e.g. the NDP.view2 and QuPath softwares.
Cells are defined by a circle outline (DAPI nuclear staining plus the FISH-generated fluorescent signal), fluorescent signals are checked channel by channel for each selected cell. Intensity, luminosity, contrast parameters are set in the software for each probe pair. DAPI (nuclear staining) was used to distinguish if two cells were located close to each other. High and low expression of each probe was analyzed, and countings collected for analysis and comparison.