1
|
Wang S, Hu M, Sun B, Pang T, Zhuang Z, Chen T. Dependence of ghost on the incident light angle into dichroic mirror. JOURNAL OF BIOPHOTONICS 2023; 16:e202300190. [PMID: 37545092 DOI: 10.1002/jbio.202300190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/17/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
The dichroic mirror (DM) is a key component in microscope. We found a ghost in the reflection channel of a dual-channel fluorescence microscope and studied the relationship between the ghost and the incidence angle θ into the DM. The DM emission surface reflection generated ghost if the θ is not45 ° . We analyzed the distance and intensity relationship between the ghost and the primary image, which is θ -dependent and was demonstrated by imaging live cells and a stage micrometer. The ghost can be eliminated by placing the DM between objective and tube lens, but not between tube lens and detector, ensuring that the incident light into the DM is approximately parallel. Furthermore, the transmitted light of the DM is shifted towards a longer wavelength with increasing θ . Collectively, microscopists must carefully optimize the θ when designing a microscope to avoid the ghost.
Collapse
Affiliation(s)
- Shuo Wang
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Min Hu
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Beini Sun
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Tian Pang
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Zhengfei Zhuang
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| | - Tongsheng Chen
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
- Guangdong Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, Guangdong, China
| |
Collapse
|
2
|
Munoz-Erazo L, Schmidt AJ, Shinko D, Price KM. How to Build an Image-Processing Pipeline for Automating Multiparameter Histocytometry Analysis. Curr Protoc 2022; 2:e380. [PMID: 35294109 DOI: 10.1002/cpz1.380] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Until relatively recently, analysis of imaging data has been primarily quantitative and limited to 3-4 markers. The advancement of various technologies overcoming this marker limitation provided the capability of analyzing multiparameter imaging data down to the single cell level, termed histocytometry. Currently, most published end-to-end histocytometric analysis of imaging data is performed using expensive commercial programs or freely available analysis packages that require significant knowledge of programming languages for execution. Here we present a protocol that performs cell segmentation, phenotyping and spatial analysis, using software with easy-to-use GUIs (graphical user interfaces). These protocols allow the user to derive spatial and phenotypical data for the analysis of multiparameter microscopic images from most imaging platforms in a low-cost manner. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Cell Segmentation and generation of histocytometric .csv file Basic Protocol 2: Phenotyping of cell populations Basic Protocol 3: Spatial relationship analyses of phenotyped populations Support Protocol 1: Nuclei Segmentation Accuracy Test Support Protocol 2: Correcting y-axis Inversion of Histocytometry Data Relative to Original Image File.
Collapse
Affiliation(s)
| | | | - Diana Shinko
- Sydney Cytometry, University of Sydney, Sydney, Australia
| | - Kylie M Price
- Malaghan Institute of Medical Research, Wellington, New Zealand
| |
Collapse
|
3
|
Pellefigues C, Naidoo K, Mehta P, Schmidt AJ, Jagot F, Roussel E, Cait A, Yumnam B, Chappell S, Meijlink K, Camberis M, Jiang JX, Painter G, Filbey K, Uluçkan Ö, Gasser O, Le Gros G. Basophils promote barrier dysfunction and resolution in the atopic skin. J Allergy Clin Immunol 2021; 148:799-812.e10. [PMID: 33662369 PMCID: PMC8410897 DOI: 10.1016/j.jaci.2021.02.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND The type 2 cytokines IL-4 and IL-13 promote not only atopic dermatitis (AD) but also the resolution of inflammation. How type 2 cytokines participate in the resolution of AD is poorly known. OBJECTIVE Our aim was to determine the mechanisms and cell types governing skin inflammation, barrier dysfunction, and resolution of inflammation in a model of AD. METHODS Mice that exhibit expression of IL-4, IL-13, and MCPT8 or that could be depleted of basophils or eosinophils, be deficient in IL-4 or MHC class II molecules, or have basophils lacking macrophage colony-stimulating factor (M-CSF) were treated with calcipotriol (MC903) as an acute model of AD. Kinetics of the disease; keratinocyte differentiation; and leukocyte accumulation, phenotype, function, and cytokine production were measured by transepidermal water loss, histopathology, molecular biology, or unbiased analysis of spectral flow cytometry. RESULTS In this model of AD, basophils were activated systemically and were the initial and main source of IL-4 in the skin. Basophils and IL-4 promoted epidermal hyperplasia and skin barrier dysfunction by acting on keratinocyte differentiation during inflammation. Basophils, IL-4, and basophil-derived M-CSF inhibited the accumulation of proinflammatory cells in the skin while promoting the expansion and function of proresolution M2-like macrophages and the expression of probarrier genes. Basophils kept their proresolution properties during AD resolution. CONCLUSION Basophils can display both beneficial and detrimental type 2 functions simultaneously during atopic inflammation.
Collapse
Affiliation(s)
- Christophe Pellefigues
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand; INSERM UMR1149, CNRS ERL8252, Centre de recherche sur l'inflammation, Inflamex, Université de Paris, Paris, France.
| | - Karmella Naidoo
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Palak Mehta
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Alfonso J Schmidt
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Ferdinand Jagot
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Elsa Roussel
- Novartis Institutes for Biomedical Research (NIBR), Novartis, Basel, Switzerland
| | - Alissa Cait
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Bibek Yumnam
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Sally Chappell
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Kimberley Meijlink
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Mali Camberis
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Jean X Jiang
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, Tex
| | - Gavin Painter
- Ferrier Research Institute, Victoria University, Wellington, New Zealand
| | - Kara Filbey
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Özge Uluçkan
- Novartis Institutes for Biomedical Research (NIBR), Novartis, Basel, Switzerland
| | - Olivier Gasser
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| | - Graham Le Gros
- Malaghan Institute of Medical Research, Victoria University, Wellington, New Zealand
| |
Collapse
|
4
|
Munoz-Erazo L, Schmidt AJ, Price KM. High-Dimensional Image Analysis using Histocytometry. Curr Protoc 2021; 1:e184. [PMID: 34165879 DOI: 10.1002/cpz1.184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Histocytometry is a technique for processing multiparameter microscopy images using computational approaches to identify and quantify cellular phenotypes. It allows for spatial analyses of cellular phenotypes in relation to each other and within defined spatial regions. The benefit of this technique over manual annotation and characterization of cells is a high degree of automation/throughput, significantly decreased user bias, and increased reproducibility. Recently, an increase in freely available software amenable to or deliberately designed for histocytometry has resulted in these complex analyses being available to a broader base of users who have amassed multi-component microscopic imaging data. This article provides an overview of a histocytometry pipeline, focusing on the strategic planning and software requirements to allow readers to perform cell segmentation, phenotyping, and spatial analyses to advance their research outputs. © 2021 Wiley Periodicals LLC.
Collapse
Affiliation(s)
| | | | - Kylie M Price
- Malaghan Institute of Medical Research, Wellington, New Zealand
| |
Collapse
|
5
|
Masci AM, White S, Neely B, Ardini-Polaske M, Hill CB, Misra RS, Aronow B, Gaddis N, Yang L, Wert SE, Palmer SM, Chan C. Ontology-guided segmentation and object identification for developmental mouse lung immunofluorescent images. BMC Bioinformatics 2021; 22:82. [PMID: 33622235 PMCID: PMC7901098 DOI: 10.1186/s12859-021-04008-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 02/08/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Immunofluorescent confocal microscopy uses labeled antibodies as probes against specific macromolecules to discriminate between multiple cell types. For images of the developmental mouse lung, these cells are themselves organized into densely packed higher-level anatomical structures. These types of images can be challenging to segment automatically for several reasons, including the relevance of biomedical context, dependence on the specific set of probes used, prohibitive cost of generating labeled training data, as well as the complexity and dense packing of anatomical structures in the image. The use of an application ontology helps surmount these challenges by combining image data with its metadata to provide a meaningful biological context, modeled after how a human expert would make use of contextual information to identify histological structures, that constrains and simplifies the process of segmentation and object identification. RESULTS We propose an innovative approach for the semi-supervised analysis of complex and densely packed anatomical structures from immunofluorescent images that utilizes an application ontology to provide a simplified context for image segmentation and object identification. We describe how the logical organization of biological facts in the form of an ontology can provide useful constraints that facilitate automatic processing of complex images. We demonstrate the results of ontology-guided segmentation and object identification in mouse developmental lung images from the Bioinformatics REsource ATlas for the Healthy lung database of the Molecular Atlas of Lung Development (LungMAP1) program CONCLUSION: We describe a novel ontology-guided approach to segmentation and classification of complex immunofluorescence images of the developing mouse lung. The ontology is used to automatically generate constraints for each image based on its biomedical context, which facilitates image segmentation and classification.
Collapse
Affiliation(s)
- Anna Maria Masci
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA.
| | - Scott White
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Ben Neely
- Duke Crucible, Duke University, Durham, NC, USA
| | | | - Carol B Hill
- Duke Clinical Research Institute, Duke School of Medicine, Durham, NC, USA
| | - Ravi S Misra
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY, USA
| | - Bruce Aronow
- Departments of Biomedical Informatics, Developmental Biology, and Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | | | - Lina Yang
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Susan E Wert
- Department of Pediatrics Perinatal Institute Divisions of Neonatology, Perinatal and Pulmonary Biology Cincinnati Children's Hospital Medical Center/Research Foundation, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Scott M Palmer
- Vice Chair for Research, Department of Medicine, Director, Respiratory Research, Duke Clinical Research Institute, Duke University Medical Center, Durham, NC, USA
| | - Cliburn Chan
- Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| |
Collapse
|
6
|
Filbey KJ, Mehta PH, Meijlink KJ, Pellefigues C, Schmidt AJ, Le Gros G. The Gastrointestinal Helminth Heligmosomoides bakeri Suppresses Inflammation in a Model of Contact Hypersensitivity. Front Immunol 2020; 11:950. [PMID: 32508831 PMCID: PMC7249854 DOI: 10.3389/fimmu.2020.00950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/22/2020] [Indexed: 01/15/2023] Open
Abstract
Helminths regulate host immune responses to ensure their own long-term survival. Numerous studies have demonstrated that these helminth-induced regulatory mechanisms can also limit host inflammatory responses in several disease models. We used the Heligmosomoides bakeri (Hb) infection model (also known as H. polygyrus or H. polygyrus bakeri in the literature) to test whether such immune regulation affects skin inflammatory responses induced by the model contact sensitiser dibutyl phthalate fluorescein isothiocynate (DBP-FITC). Skin lysates from DBP-FITC-sensitized, Hb-infected mice produced less neutrophil specific chemokines and had significantly reduced levels of skin thickening and cellular inflammatory responses in tissue and draining lymph nodes (LNs) compared to uninfected mice. Hb-induced suppression did not appear to be mediated by regulatory T cells, nor was it due to impaired dendritic cell (DC) activity. Mice cleared of infection remained unresponsive to DBP-FITC sensitization indicating that suppression was not via the secretion of Hb-derived short-lived regulatory molecules, although long-term effects on cells cannot be ruled out. Importantly, similar helminth-induced suppression of inflammation was also seen in the draining LN after intradermal injection of the ubiquitous allergen house dust mite (HDM). These findings demonstrate that Hb infection attenuates skin inflammatory responses by suppressing chemokine production and recruitment of innate cells. These findings further contribute to the growing body of evidence that helminth infection can modulate inflammatory and allergic responses via a number of mechanisms with potential to be exploited in therapeutic and preventative strategies in the future.
Collapse
Affiliation(s)
- Kara J Filbey
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Palak H Mehta
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | | | | | - Graham Le Gros
- Malaghan Institute of Medical Research, Wellington, New Zealand
| |
Collapse
|
7
|
Ferrer-Font L, Mehta P, Harmos P, Schmidt AJ, Chappell S, Price KM, Hermans IF, Ronchese F, le Gros G, Mayer JU. High-dimensional analysis of intestinal immune cells during helminth infection. eLife 2020; 9:51678. [PMID: 32041687 PMCID: PMC7012606 DOI: 10.7554/elife.51678] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 01/15/2020] [Indexed: 12/13/2022] Open
Abstract
Single cell isolation from helminth-infected murine intestines has been notoriously difficult, due to the strong anti-parasite type 2 immune responses that drive mucus production, tissue remodeling and immune cell infiltration. Through the systematic optimization of a standard intestinal digestion protocol, we were able to successfully isolate millions of immune cells from the heavily infected duodenum. To validate that these cells gave an accurate representation of intestinal immune responses, we analyzed them using a high-dimensional spectral flow cytometry panel and confirmed our findings by confocal microscopy. Our cell isolation protocol and high-dimensional analysis allowed us to identify many known hallmarks of anti-parasite immune responses throughout the entire course of helminth infection and has the potential to accelerate single-cell discoveries of local helminth immune responses that have previously been unfeasible.
Collapse
Affiliation(s)
| | - Palak Mehta
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Phoebe Harmos
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | | - Sally Chappell
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Kylie M Price
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Ian F Hermans
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Franca Ronchese
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Graham le Gros
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | | |
Collapse
|