PUPAID: A R + ImageJ pipeline for thorough and semi-automated processing and analysis of multi-channel immunofluorescence data

• Paul Régnier ,

  Roles Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Resources, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: paul.regnier@aphp.fr, paul.regnier@sorbonne-universite.fr

  Affiliations Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France, Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France

  https://orcid.org/0000-0002-9713-1132

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• Camille Montardi ,

  Contributed equally to this work with: Camille Montardi, Anna Maciejewski-Duval

  Roles Formal analysis, Investigation

  Affiliation Département de Médecine Interne, Hôpital Ambroise Paré, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Saclay, Boulogne-Billancourt, France

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• Anna Maciejewski-Duval ,

  Contributed equally to this work with: Camille Montardi, Anna Maciejewski-Duval

  Roles Data curation, Formal analysis, Investigation, Methodology, Project administration, Resources, Supervision

  Affiliations Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France, Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France

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• Cindy Marques,

  Roles Resources, Writing – original draft

  Affiliations Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France, Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France, Département de Médecine Interne et Immunologie Clinique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France, Centre National de Référence Maladies Autoimmunes Systémiques Rares, Centre National de Référence Maladies Autoinflammatoires et Amylose Inflammatoire, Inflammation-Immunopathology-Biotherapy Department (DMU 3iD), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France

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• David Saadoun

  Roles Project administration, Supervision, Writing – original draft

  Affiliations Immunology-Immunopathology-Immunotherapy (i3) Laboratory, INSERM UMR-S 959, Sorbonne Université, Paris, France, Biotherapy Unit (CIC-BTi), Inflammation-Immunopathology-Biotherapy Department (DHU i2B), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France, Département de Médecine Interne et Immunologie Clinique, Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France, Centre National de Référence Maladies Autoimmunes Systémiques Rares, Centre National de Référence Maladies Autoinflammatoires et Amylose Inflammatoire, Inflammation-Immunopathology-Biotherapy Department (DMU 3iD), Groupe Hospitalier Pitié-Salpêtrière, Assistance Publique-Hôpitaux de Paris (AP-HP), Sorbonne Université, Paris, France

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