1
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Usability of deep learning pipelines for 3D nuclei identification with Stardist and Cellpose. Cells Dev 2022; 172:203806. [PMID: 36029974 DOI: 10.1016/j.cdev.2022.203806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 07/21/2022] [Accepted: 08/22/2022] [Indexed: 01/25/2023]
Abstract
Segmentation of 3D images to identify cells and their molecular outputs can be difficult and tedious. Machine learning algorithms provide a promising alternative to manual analysis as emerging 3D image processing technology can save considerable time. For those unfamiliar with machine learning or 3D image analysis, the rapid advancement of the field can make navigating the newest software options confusing. In this paper, two open-source machine learning algorithms, Cellpose and Stardist, are compared in their application on a 3D light sheet dataset counting fluorescently stained proliferative cell nuclei. The effects of image tiling and background subtraction are shown through image analysis pipelines for both algorithms. Based on our analysis, the relative ease of use of Cellpose and the absence of need to train a model leaves it a strong option for 3D cell segmentation despite relatively longer processing times. When Cellpose's pretrained model yields results that are not of sufficient quality, or the analysis of a large dataset is required, Stardist may be more appropriate. Despite the time it takes to train the model, Stardist can create a model specialized to the users' dataset that can be iteratively improved until predictions are satisfactory with far lower processing time relative to other methods.
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2
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Haggerty AE, Maldonado-Lasunción I, Nitobe Y, Yamane K, Marlow MM, You H, Zhang C, Cho B, Li X, Reddy S, Mao HQ, Oudega M. The Effects of the Combination of Mesenchymal Stromal Cells and Nanofiber-Hydrogel Composite on Repair of the Contused Spinal Cord. Cells 2022; 11:cells11071137. [PMID: 35406701 PMCID: PMC8997442 DOI: 10.3390/cells11071137] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 02/01/2023] Open
Abstract
A bone marrow-derived mesenchymal stromal cell (MSC) transplant and a bioengineered nanofiber-hydrogel composite (NHC) have been shown to stimulate nervous tissue repair in the contused spinal cord in rodent models. Here, these two modalities were combined to assess their repair effects in the contused spinal cord in adult rats. Cohorts of contused rats were treated with MSC in NHC (MSC-NHC), MSC in phosphate-buffered saline (MSC-PBS), NHC, or PBS injected into the contusion site at 3 days post-injury. One week after injury, there were significantly fewer CD68+ cells in the contusion with MSC-NHC and NHC, but not MSC-PBS. The reduction in CD86+ cells in the injury site with MSC-NHC was mainly attributed to NHC. One and eight weeks after injury, we found a greater CD206+/CD86+ cell ratio with MSC-NHC or NHC, but not MSC-PBS, indicating a shift from a pro-inflammatory towards an anti-inflammatory milieu in the injury site. Eight weeks after injury, the injury size was significantly reduced with MSC-NHC, NHC, and MSC-PBS. At this time, astrocyte, and axon presence in the injury site was greater with MSC-NHC compared with MSC-PBS. We did not find a significant effect of NHC on MSC transplant survival, and hind limb function was similar across all groups. However, we did find fewer macrophages at 1 week post-injury, more macrophages polarized towards a pro-regenerative phenotype at 1 and 8 weeks after injury, and reduced injury volume, more astrocytes, and more axons at 8 weeks after injury in rats with MSC-NHC and NHC alone compared with MSC-PBS; these findings were especially significant between rats with MSC-NHC and MSC-PBS. The data support further study in the use of an NHC-MSC combination transplant in the contused spinal cord.
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Affiliation(s)
- Agnes E. Haggerty
- The Miami Project to Cure Paralysis, University of Miami, Miami, FL 33136, USA; (A.E.H.); (I.M.-L.); (Y.N.); (K.Y.); (M.M.M.)
| | - Ines Maldonado-Lasunción
- The Miami Project to Cure Paralysis, University of Miami, Miami, FL 33136, USA; (A.E.H.); (I.M.-L.); (Y.N.); (K.Y.); (M.M.M.)
- Department of Regeneration of Sensorimotor Systems, Netherlands Institute for Neuroscience, Institute of the Royal Netherlands Academy of Arts and Sciences, 1105 BA Amsterdam, The Netherlands
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Therapy and Human Movements Sciences, Northwestern University, Chicago, IL 60611, USA
| | - Yohshiro Nitobe
- The Miami Project to Cure Paralysis, University of Miami, Miami, FL 33136, USA; (A.E.H.); (I.M.-L.); (Y.N.); (K.Y.); (M.M.M.)
- Department of Orthopedic Surgery, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Kentaro Yamane
- The Miami Project to Cure Paralysis, University of Miami, Miami, FL 33136, USA; (A.E.H.); (I.M.-L.); (Y.N.); (K.Y.); (M.M.M.)
- Department of Orthopedic Surgery, Okayama University Graduate School of Medicine, Dentistry, and Pharmaceutical Science, Kitaku, Okayama 700-8558, Japan
| | - Megan M. Marlow
- The Miami Project to Cure Paralysis, University of Miami, Miami, FL 33136, USA; (A.E.H.); (I.M.-L.); (Y.N.); (K.Y.); (M.M.M.)
| | - Hua You
- Department of Oncology and Hematology, Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou 510095, China;
| | - Chi Zhang
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA; (C.Z.); (B.C.); (X.L.)
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA;
| | - Brian Cho
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA; (C.Z.); (B.C.); (X.L.)
- Department of Plastic and Reconstructive Surgery, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
| | - Xiaowei Li
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA; (C.Z.); (B.C.); (X.L.)
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA;
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Sashank Reddy
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA;
- Department of Plastic and Reconstructive Surgery, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hai-Quan Mao
- Translational Tissue Engineering Center, Johns Hopkins School of Medicine, Baltimore, MD 21231, USA; (C.Z.); (B.C.); (X.L.)
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA;
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA
- Correspondence: (H.-Q.M.); (M.O.)
| | - Martin Oudega
- Shirley Ryan AbilityLab, Chicago, IL 60611, USA
- Department of Physical Therapy and Human Movements Sciences, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University, Chicago, IL 60611, USA
- Edward Hines Jr. VA Hospital, Hines, IL 60141, USA
- Correspondence: (H.-Q.M.); (M.O.)
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3
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Yang L, Pijuan-Galito S, Rho HS, Vasilevich AS, Eren AD, Ge L, Habibović P, Alexander MR, de Boer J, Carlier A, van Rijn P, Zhou Q. High-Throughput Methods in the Discovery and Study of Biomaterials and Materiobiology. Chem Rev 2021; 121:4561-4677. [PMID: 33705116 PMCID: PMC8154331 DOI: 10.1021/acs.chemrev.0c00752] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Indexed: 02/07/2023]
Abstract
The complex interaction of cells with biomaterials (i.e., materiobiology) plays an increasingly pivotal role in the development of novel implants, biomedical devices, and tissue engineering scaffolds to treat diseases, aid in the restoration of bodily functions, construct healthy tissues, or regenerate diseased ones. However, the conventional approaches are incapable of screening the huge amount of potential material parameter combinations to identify the optimal cell responses and involve a combination of serendipity and many series of trial-and-error experiments. For advanced tissue engineering and regenerative medicine, highly efficient and complex bioanalysis platforms are expected to explore the complex interaction of cells with biomaterials using combinatorial approaches that offer desired complex microenvironments during healing, development, and homeostasis. In this review, we first introduce materiobiology and its high-throughput screening (HTS). Then we present an in-depth of the recent progress of 2D/3D HTS platforms (i.e., gradient and microarray) in the principle, preparation, screening for materiobiology, and combination with other advanced technologies. The Compendium for Biomaterial Transcriptomics and high content imaging, computational simulations, and their translation toward commercial and clinical uses are highlighted. In the final section, current challenges and future perspectives are discussed. High-throughput experimentation within the field of materiobiology enables the elucidation of the relationships between biomaterial properties and biological behavior and thereby serves as a potential tool for accelerating the development of high-performance biomaterials.
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Affiliation(s)
- Liangliang Yang
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Sara Pijuan-Galito
- School
of Pharmacy, Biodiscovery Institute, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Hoon Suk Rho
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aliaksei S. Vasilevich
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aysegul Dede Eren
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Lu Ge
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Pamela Habibović
- Department
of Instructive Biomaterials Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Morgan R. Alexander
- School
of Pharmacy, Boots Science Building, University
of Nottingham, University Park, Nottingham NG7 2RD, U.K.
| | - Jan de Boer
- Department
of Biomedical Engineering, Eindhoven University
of Technology, 5600 MB Eindhoven, The Netherlands
| | - Aurélie Carlier
- Department
of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired
Regenerative Medicine, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Patrick van Rijn
- University
of Groningen, W. J. Kolff Institute for Biomedical Engineering and
Materials Science, Department of Biomedical Engineering, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Qihui Zhou
- Institute
for Translational Medicine, Department of Stomatology, The Affiliated
Hospital of Qingdao University, Qingdao
University, Qingdao 266003, China
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Characteristics and antitumor activity of polysorbate 80 curcumin micelles preparation by cloud point cooling. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2020.101871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Browning JR, Derr P, Derr K, Doudican N, Michael S, Lish SR, Taylor NA, Krueger JG, Ferrer M, Carucci JA, Gareau DS. A 3D biofabricated cutaneous squamous cell carcinoma tissue model with multi-channel confocal microscopy imaging biomarkers to quantify antitumor effects of chemotherapeutics in tissue. Oncotarget 2020; 11:2587-2596. [PMID: 32676161 PMCID: PMC7343636 DOI: 10.18632/oncotarget.27570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 04/03/2020] [Indexed: 11/25/2022] Open
Abstract
Cutaneous squamous cell carcinoma (cSCC) causes approximately 10,000 deaths annually in the U. S. Current therapies are largely ineffective against metastatic and locally advanced cSCC. There is a need to identify novel, effective, and less toxic small molecule cSCC therapeutics. We developed a 3-dimensional bioprinted skin (3DBPS) model of cSCC tumors together with a microscopy assay to test chemotherapeutic effects in tissue. The full thickness SCC tissue model was validated using hematoxylin and eosin (H&E) and immunohistochemical histological staining, confocal microscopy, and cDNA microarray analysis. A nondestructive, 3D fluorescence confocal imaging assay with tdTomato-labeled A431 SCC and ZsGreen-labeled keratinocytes was developed to test efficacy and general toxicity of chemotherapeutics. Fluorescence-derived imaging biomarkers indicated that 50% of cancer cells were killed in the tissue after 1μM 5-Fluorouracil 48-hour treatment, compared to a baseline of 12% for untreated controls. The imaging biomarkers also showed that normal keratinocytes were less affected by treatment (11% killed) than the untreated tissue, which had no significant killing effect. Data showed that 5-Fluorouracil selectively killed cSCC cells more than keratinocytes. Our 3DBPS assay platform provides cellular-level measurement of cell viability and can be adapted to achieve nondestructive high-throughput screening (HTS) in bio-fabricated tissues.
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Affiliation(s)
- James R Browning
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Paige Derr
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Kristy Derr
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Nicole Doudican
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, New York, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Samantha R Lish
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Nicholas A Taylor
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, New York, USA
| | - James G Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
| | - Marc Ferrer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - John A Carucci
- The Ronald O. Perelman Department of Dermatology, New York University School of Medicine, New York, New York, USA
| | - Daniel S Gareau
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, New York, USA
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6
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Chu L, Luo Y, Chen H, Miao Q, Wang L, Moats R, Wang T, Kennedy JC, Henske EP, Shi W. Mesenchymal folliculin is required for alveolar development: implications for cystic lung disease in Birt-Hogg-Dubé syndrome. Thorax 2020; 75:486-493. [PMID: 32238524 DOI: 10.1136/thoraxjnl-2019-214112] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/13/2020] [Accepted: 03/18/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Pulmonary cysts and spontaneous pneumothorax are presented in most patients with Birt-Hogg-Dubé (BHD) syndrome, which is caused by loss of function mutations in the folliculin (FLCN) gene. The pathogenic mechanisms underlying the cystic lung disease in BHD are poorly understood. METHODS Mesenchymal Flcn was specifically deleted in mice or in cultured lung mesenchymal progenitor cells using a Cre/loxP approach. Dynamic changes in lung structure, cellular and molecular phenotypes and signalling were measured by histology, immunofluorescence staining and immunoblotting. RESULTS Deletion of Flcn in mesoderm-derived mesenchymal cells results in significant reduction of postnatal alveolar growth and subsequent alveolar destruction, leading to cystic lesions. Cell proliferation and alveolar myofibroblast differentiation are inhibited in the Flcn knockout lungs, and expression of the extracellular matrix proteins Col3a1 and elastin are downregulated. Signalling pathways including mTORC1, AMP-activated protein kinase, ERK1/2 and Wnt-β-catenin are differentially affected at different developmental stages. All the above changes have statistical significance (p<0.05). CONCLUSIONS Mesenchymal Flcn is an essential regulator during alveolar development and maintenance, through multiple cellular and molecular mechanisms. The mesenchymal Flcn knockout mouse model provides the first in vivo disease model that may recapitulate the stages of cyst development in human BHD. These findings elucidate the developmental origins and mechanisms of lung disease in BHD.
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Affiliation(s)
- Ling Chu
- The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.,The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Yongfeng Luo
- The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Hui Chen
- The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Qing Miao
- The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Larry Wang
- The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Rex Moats
- The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Tiansheng Wang
- The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - John C Kennedy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Elizabeth P Henske
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Wei Shi
- The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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7
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Powell JM, Plummer NW, Scappini EL, Tucker CJ, Jensen P. DEFiNE: A Method for Enhancement and Quantification of Fluorescently Labeled Axons. Front Neuroanat 2019; 12:117. [PMID: 30687025 PMCID: PMC6336715 DOI: 10.3389/fnana.2018.00117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/17/2018] [Indexed: 11/29/2022] Open
Abstract
Visualization and quantification of fluorescently labeled axonal fibers are widely employed in studies of neuronal connectivity in the brain. However, accurate analysis of axon density is often confounded by autofluorescence and other fluorescent artifacts. By the time these problems are detected in labeled tissue sections, significant time and resources have been invested, and the tissue may not be easy to replace. In response to these difficulties, we have developed Digital Enhancement of Fibers with Noise Elimination (DEFiNE), a method for eliminating fluorescent artifacts from digital images based on their morphology and fluorescence spectrum, thus permitting enhanced visualization and quantification of axonal fibers. Application of this method is facilitated by a DEFiNE macro, written using ImageJ Macro Language (IJM), which includes an automated and customizable procedure for image processing and a semi-automated quantification method that accounts for any remaining local variation in background intensity. The DEFiNE macro is open-source and used with the widely available FIJI software for maximum accessibility.
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Affiliation(s)
- Jeanne M Powell
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Nicholas W Plummer
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Erica L Scappini
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Charles J Tucker
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
| | - Patricia Jensen
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, United States Department of Health and Human Services, Durham, NC, United States
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