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Ohlsson JA, Leong JX, Elander PH, Ballhaus F, Holla S, Dauphinee AN, Johansson J, Lommel M, Hofmann G, Betnér S, Sandgren M, Schumacher K, Bozhkov PV, Minina EA. SPIRO - the automated Petri plate imaging platform designed by biologists, for biologists. Plant J 2024; 118:584-600. [PMID: 38141174 DOI: 10.1111/tpj.16587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/04/2023] [Indexed: 12/25/2023]
Abstract
Phenotyping of model organisms grown on Petri plates is often carried out manually, despite the procedures being time-consuming and laborious. The main reason for this is the limited availability of automated phenotyping facilities, whereas constructing a custom automated solution can be a daunting task for biologists. Here, we describe SPIRO, the Smart Plate Imaging Robot, an automated platform that acquires time-lapse photographs of up to four vertically oriented Petri plates in a single experiment, corresponding to 192 seedlings for a typical root growth assay and up to 2500 seeds for a germination assay. SPIRO is catered specifically to biologists' needs, requiring no engineering or programming expertise for assembly and operation. Its small footprint is optimized for standard incubators, the inbuilt green LED enables imaging under dark conditions, and remote control provides access to the data without interfering with sample growth. SPIRO's excellent image quality is suitable for automated image processing, which we demonstrate on the example of seed germination and root growth assays. Furthermore, the robot can be easily customized for specific uses, as all information about SPIRO is released under open-source licenses. Importantly, uninterrupted imaging allows considerably more precise assessment of seed germination parameters and root growth rates compared with manual assays. Moreover, SPIRO enables previously technically challenging assays such as phenotyping in the dark. We illustrate the benefits of SPIRO in proof-of-concept experiments which yielded a novel insight on the interplay between autophagy, nitrogen sensing, and photoblastic response.
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Affiliation(s)
- Jonas A Ohlsson
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Jia Xuan Leong
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, 72076, Germany
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Auf der Morgenstelle 32, Tübingen, D-72076, Germany
| | - Pernilla H Elander
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Florentine Ballhaus
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Sanjana Holla
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Adrian N Dauphinee
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | | | - Mark Lommel
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
- Department of Microbiology, Saarland University, Campus A1.5, Saarbrücken, 66123, Germany
| | - Gero Hofmann
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Staffan Betnér
- Northern Registry Centre, Department of Public Health and Clinical Medicine, Umeå University, Umeå, 90187, Sweden
| | - Mats Sandgren
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Karin Schumacher
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
| | - Elena A Minina
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, SE-750 07, Sweden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, 69120, Germany
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Jurberg AD, Gomes G, Seixas MR, Mermelstein C, Costa ML. Improving quantification of myotube width and nuclear/cytoplasmic ratio in myogenesis research. Comput Methods Programs Biomed 2023; 230:107354. [PMID: 36682109 DOI: 10.1016/j.cmpb.2023.107354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND AND OBJECTIVE The culture of skeletal muscle cells is particularly relevant to basic biomedical research and translational medicine. The incubation of dissociated cells under controlled conditions has helped to dissect several molecular mechanisms associated with muscle cell differentiation, in addition to contributing for the evaluation of drug effects and prospective cell therapies for patients with degenerative muscle pathologies. The formation of mature multinucleated myotubes is a stepwise process involving well defined events of cell proliferation, commitment, migration, and fusion easily identified through optical microscopy methods including immunofluorescence and live cell imaging. The characterization of each step is usually based on muscle cell morphology and nuclei number, as well as the presence and intracellular location of specific cell markers. However, manual quantification of these parameters in large datasets of images is work-intensive and prone to researcher's subjectivity, mostly because of the extremely elongated cell shape of large myotubes and because myotubes are multinucleated. METHODS Here we provide two semi-automated ImageJ macros aimed to measure the width of myotubes and the nuclear/cytoplasmic localization of molecules in fluorescence images. The width measuring macro automatically determines the best angle, perpendicular to most cells, to draw a profile plot and identify and measure individual myotubes. The nuclear/cytoplasmic ratio macro compares the intensity values along lines, drawn by the user, over cytoplasm and nucleus. RESULTS We show that the macro measurements are more consistent than manual measurements by comparing with our own results and with the literature. CONCLUSIONS By relying on semi-automated muscle specific ImageJ macros, we seek to improve measurement accuracy and to alleviate the laborious routine of counting and measuring muscle cell features.
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Affiliation(s)
- Arnon Dias Jurberg
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil; Instituto de Educação Médica (IDOMED), Campus Vista Carioca, Universidade Estácio de Sá (UNESA), RJ, Brazil
| | - Geyse Gomes
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Marianna Reis Seixas
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Claudia Mermelstein
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil
| | - Manoel Luis Costa
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Brazil.
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Anania JC, Westin A, Adler J, Heyman B. A Novel Image Analysis Approach Reveals a Role for Complement Receptors 1 and 2 in Follicular Dendritic Cell Organization in Germinal Centers. Front Immunol 2021; 12:655753. [PMID: 33912182 PMCID: PMC8072117 DOI: 10.3389/fimmu.2021.655753] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/22/2021] [Indexed: 11/15/2022] Open
Abstract
Follicular dendritic cells (FDCs) are rare and enigmatic cells that mainly reside in germinal centers (GCs). They are capable of capturing immune complexes, via their Fc (FcRs) and complement receptors (CRs) and storing them for long periods in non-degradative vesicles. Presentation of ICs on FDCs to B cells is believed to drive affinity maturation. CR1 and CR2 are expressed on B cells and FDCs. Cr2 knock out (KO) mice, lacking both receptors, have impaired antibody and GC responses. Utilizing a novel ImageJ macro to analyze confocal fluorescence microscopy images of spleen sections, we here investigate how FDCs in wild type (WT) and Cr2 KO mice behave during the first two weeks after immunization with sheep red blood cells (SRBC). Mice were immunized with SRBC i.v. and spleen and serum samples harvested at various time points. As expected, antibody and GC responses in Cr2 KO mice were impaired in comparison to WT mice. Fewer FDCs were identified in Cr2 KO mice, and these exhibited differential localization and organization in comparison to WT mice. WT FDCs were primarily located within GCs at the light zone/dark zone border. FDCs from WT but not Cr2 KO mice were actively dispersed in GCs, i.e. tended to move away from each other, presumably to increase their surface area for B cell interaction. FDCs from Cr2 KO mice were more often found on follicles outside of the GCs and those within the GCs were closer to the periphery in comparison to WT FDCs. Expression of CR1 and CR2, FcγRIIB, and FcµR increased in FDCs from WT mice during the course of immunization. The results suggest that decreased ability to capture ICs by FDCs lacking CR1 and CR2 may not be the only explanation for the impaired GC and antibody responses in Cr2 KO mice. Poor FDC organization in GCs and failure to increase receptor expression after immunization may further contribute to the inefficient immune responses observed.
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Affiliation(s)
- Jessica C. Anania
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Annika Westin
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jeremy Adler
- Department of Immunology, Genetics and Pathology, Facilities, BioVis, Uppsala University, Uppsala, Sweden
| | - Birgitta Heyman
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Nakamura M, Kamehama T, Sato Y. Image analysis of stress-induced lignin deposition in Arabidopsis thaliana using the macro program LigninJ for ImageJ software. Plant Biotechnol (Tokyo) 2020; 37:105-109. [PMID: 32362756 PMCID: PMC7193838 DOI: 10.5511/plantbiotechnology.20.0110a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
In vascular plants, lignin is deposited during morphogenesis but also under stress conditions. Assessing the degree of stress-induced lignin deposition is complicated because it occurs locally and irregularly in plant tissues. In this study, we developed a macro program, LigninJ, for the open-source software ImageJ to automatically and efficiently determine areas and levels of lignification after Wiesner (phloroglucinol-HCl) staining. We used the CIELAB color space for detection of red color following the Wiesner reaction. In addition, LigninJ has a function for adjusting the background level and its white balance to reduce biases that are inherent to individual color images. Furthermore, LigninJ can be used for batch analyses of multiple images, taking about 2 s per image. In this study, we analyzed wound-induced lignin deposition in cotyledons of the Arabidopsis thaliana ecotypes Landsberg erecta and Columbia and assessed ectopic lignin depositions in roots of lignescence (lig) mutants of Arabidopsis. Our results confirmed that this method is efficient for evaluating the degree of stress-induced lignin deposition.
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Affiliation(s)
- Masato Nakamura
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790–8577, Japan
| | - Tomoaki Kamehama
- Faculty of Science, Ehime University, Matsuyama, Ehime 790–8577, Japan
| | - Yasushi Sato
- Graduate School of Science and Engineering, Ehime University, Matsuyama, Ehime 790–8577, Japan
- E-mail: Tel: +81-89-927-9633 Fax: +81-89-927-9630
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Cacciabue M, Currá A, Gismondi MI. ViralPlaque: a Fiji macro for automated assessment of viral plaque statistics. PeerJ 2019; 7:e7729. [PMID: 31579606 PMCID: PMC6764358 DOI: 10.7717/peerj.7729] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/22/2019] [Indexed: 12/11/2022] Open
Abstract
Plaque assay has been used for a long time to determine infectious titers and characterize prokaryotic and eukaryotic viruses forming plaques. Indeed, plaque morphology and dimensions can provide information regarding the replication kinetics and the virulence of a particular virus. In this work, we present ViralPlaque, a fast, open-source and versatile ImageJ macro for the automated determination of viral plaque dimensions from digital images. Also, a machine learning plugin is integrated in the analysis algorithm for adaptation of ViralPlaque to the user's needs and experimental conditions. A high correlation between manual and automated measurements of plaque dimensions was demonstrated. This macro will facilitate reliable and reproducible characterization of cytolytic viruses with an increased processing speed.
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Affiliation(s)
- Marco Cacciabue
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina.,Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
| | - Anabella Currá
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina.,Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
| | - Maria I Gismondi
- Instituto de Agrobiotecnología y Biología Molecular (IABiMo), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina.,Departamento de Ciencias Básicas, Universidad Nacional de Luján, Luján, Buenos Aires, Argentina
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Boix-Fabrés J, Karkali K, Martín-Blanco E, Rebollo E. Automated Macro Approach to Remove Vitelline Membrane Autofluorescence in Drosophila Embryo 4D Movies. Methods Mol Biol 2019; 2040:155-175. [PMID: 31432480 DOI: 10.1007/978-1-4939-9686-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
This chapter provides an ImageJ/Fiji automated macro approach to remove the vitelline membrane autofluorescence in live Drosophila embryo movies acquired in a 4D (3D plus time) fashion. The procedure consists in a segmentation pipeline that can cope with different relative intensities of the vitelline membrane autofluorescence, followed by a developed algorithm that adjusts the extracted outline selection to the shape deformations that naturally occur during Drosophila embryo development. Finally, the fitted selection is used to clear the external glowing halo that, otherwise, would obscure the visualization of the internal embryo labeling upon projection or 3D rendering.
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Affiliation(s)
- Jaume Boix-Fabrés
- Molecular Imaging Platform, Molecular Biology Institute of Barcelona, Spanish National Research Council (CSIC), Barcelona, Spain
| | - Katerina Karkali
- Molecular Biology Institute of Barcelona (IBMB-CSIC), Barcelona, Spain
| | | | - Elena Rebollo
- Molecular Imaging Platform, Molecular Biology Institute of Barcelona (CSIC), Barcelona, Spain.
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Dias RA, Gonçalves BP, da Rocha JF, da Cruz E Silva OAB, da Silva AMF, Vieira SI. NeuronRead, an open source semi-automated tool for morphometric analysis of phase contrast and fluorescence neuronal images. Mol Cell Neurosci 2017; 85:57-69. [PMID: 28847569 DOI: 10.1016/j.mcn.2017.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 07/07/2017] [Accepted: 08/10/2017] [Indexed: 11/30/2022] Open
Abstract
Neurons are specialized cells of the Central Nervous System whose function is intricately related to the neuritic network they develop to transmit information. Morphological evaluation of this network and other neuronal structures is required to establish relationships between neuronal morphology and function, and may allow monitoring physiological and pathophysiologic alterations. Fluorescence-based microphotographs are the most widely used in cellular bioimaging, but phase contrast (PhC) microphotographs are easier to obtain, more affordable, and do not require invasive, complicated and disruptive techniques. Despite the various freeware tools available for fluorescence-based images analysis, few exist that can tackle the more elusive and harder-to-analyze PhC images. To surpass this, an interactive semi-automated image processing workflow was developed to easily extract relevant information (e.g. total neuritic length, average cell body area) from both PhC and fluorescence neuronal images. This workflow, named 'NeuronRead', was developed in the form of an ImageJ macro. Its robustness and adaptability were tested and validated on rat cortical primary neurons under control and differentiation inhibitory conditions. Validation included a comparison to manual determinations and to a golden standard freeware tool for fluorescence image analysis. NeuronRead was subsequently applied to PhC images of neurons at distinct differentiation days and exposed or not to DAPT, a pharmacological inhibitor of the γ-secretase enzyme, which cleaves the well-known Alzheimer's amyloid precursor protein (APP) and the Notch receptor. Data obtained confirms a neuritogenic regulatory role for γ-secretase products and validates NeuronRead as a time- and cost-effective useful monitoring tool.
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Affiliation(s)
- Roberto A Dias
- Cell Differentiation and Regeneration group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal; Neurosciences and Signalling group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal
| | - Bruno P Gonçalves
- Cell Differentiation and Regeneration group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal; Neurosciences and Signalling group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal
| | - Joana F da Rocha
- Cell Differentiation and Regeneration group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal; Neurosciences and Signalling group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal
| | - Odete A B da Cruz E Silva
- Neurosciences and Signalling group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal
| | - Augusto M F da Silva
- Instituto de Engenharia Electrónica e Telemática (IEETA), Departamento de Electrónica e Telecomunicações (DETI), Universidade de Aveiro, Aveiro, Portugal
| | - Sandra I Vieira
- Cell Differentiation and Regeneration group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal; Neurosciences and Signalling group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, Universidade de Aveiro, Aveiro, Portugal.
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