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"global_sentence_id": 72, "edu_l1_label": "EDU_O"}, {"txt": " Python/napari and R/Shiny are the connecting partners that form the analysis framework.", "language": "english", "position": {"atoms": [{"position_id": 1723, "txt": " Python/napari and R/Shiny are the connecting partners that form the analysis framework.", "x": "/html/body/div[2]/main/article/div[3]/div[1]/section[2]/div/div/div[1]/figure/div[1]/div[2]/p/b[3]"}]}, "tags": ["b", "img"], "label": "figure_title", "web_segment_id": 25, "global_sentence_id": 73, "edu_l1_label": "EDU_O"}, {"txt": " d Example images and segmentation results for various 2D, 3D and 4D imaging modalities to demonstrate the broad capability of the Cecelia framework.", "language": "english", "position": {"atoms": [{"position_id": 1724, "txt": " ", "x": "/html/body/div[2]/main/article/div[3]/div[1]/section[2]/div/div/div[1]/figure/div[1]/div[2]/p/b[3]"}, {"position_id": 1726, "txt": "d", "x": 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"/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[1]/p[1]"}, {"position_id": 3177, "txt": "FEBS Lett.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[1]/p[1]/i"}, {"position_id": 3179, "txt": "596", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[1]/p[1]/b"}, {"position_id": 3181, "txt": ", 2472–2485 (2022).", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[1]/p[1]/b"}]}, "tags": ["li", "b"], "label": "reference", "web_segment_id": 143, "global_sentence_id": 591, "edu_l1_label": "EDU_O"}, {"txt": "Leal, J. 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Appl.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[20]/p[1]/i"}]}, "tags": ["li"], "label": "reference", "web_segment_id": 162, "global_sentence_id": 667, "edu_l1_label": "EDU_O"}, {"txt": " Stat.28, 100–108 (1979).", "language": "english", "position": {"atoms": [{"position_id": 3389, "txt": " Stat.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[20]/p[1]/i"}, {"position_id": 3391, "txt": "28", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[20]/p[1]/b"}, {"position_id": 3393, "txt": ", 100–108 (1979).", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[20]/p[1]/b"}]}, "tags": ["b", "li"], "label": "reference", "web_segment_id": 162, "global_sentence_id": 668, "edu_l1_label": "EDU_O"}, {"txt": "Black, S. et al.", "language": "english", "position": {"atoms": [{"position_id": 3395, "txt": "Black, S. et al.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]"}]}, "tags": ["li"], "label": "reference", "web_segment_id": 163, "global_sentence_id": 669, "edu_l1_label": "EDU_O"}, {"txt": " CODEX multiplexed tissue imaging with DNA-conjugated antibodies.", "language": "english", "position": {"atoms": [{"position_id": 3396, "txt": " CODEX multiplexed tissue imaging with DNA-conjugated antibodies.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]"}]}, "tags": ["li"], "label": "reference", "web_segment_id": 163, "global_sentence_id": 670, "edu_l1_label": "EDU_O"}, {"txt": " Nat.", "language": "english", "position": {"atoms": [{"position_id": 3397, "txt": " ", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]"}, {"position_id": 3399, "txt": "Nat.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]/i"}]}, "tags": ["li"], "label": "reference", "web_segment_id": 163, "global_sentence_id": 671, "edu_l1_label": "EDU_O"}, {"txt": " Protoc.16, 3802–3835 (2021).", "language": "english", "position": {"atoms": [{"position_id": 3400, "txt": " Protoc.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]/i"}, {"position_id": 3402, "txt": "16", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]/b"}, {"position_id": 3404, "txt": ", 3802–3835 (2021).", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[21]/p[1]/b"}]}, "tags": ["li", "b"], "label": "reference", "web_segment_id": 163, "global_sentence_id": 672, "edu_l1_label": "EDU_O"}, {"txt": "Goltsev, Y. et al.", "language": "english", "position": {"atoms": [{"position_id": 3406, "txt": "Goltsev, Y. et al.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[22]/p[1]"}]}, "tags": ["li"], "label": "reference", "web_segment_id": 164, "global_sentence_id": 673, "edu_l1_label": "EDU_O"}, {"txt": " Deep profiling of mouse splenic architecture with CODEX multiplexed imaging.", "language": "english", "position": {"atoms": [{"position_id": 3407, "txt": " Deep profiling of mouse splenic architecture with CODEX multiplexed imaging.", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[22]/p[1]"}]}, "tags": ["li"], "label": "reference", "web_segment_id": 164, "global_sentence_id": 674, "edu_l1_label": "EDU_O"}, {"txt": " Cell174, 968–981.e915 (2018).", "language": "english", "position": {"atoms": [{"position_id": 3408, "txt": " ", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[22]/p[1]"}, {"position_id": 3410, "txt": "Cell", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[22]/p[1]/i"}, {"position_id": 3412, "txt": "174", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[22]/p[1]/b"}, {"position_id": 3414, "txt": ", 968–981.e915 (2018).", "x": "/html/body/div[2]/main/article/div[3]/div[2]/div/section/div/div/div/ol/li[22]/p[1]/b"}]}, "tags": ["b", "li"], "label": "reference", "web_segment_id": 164, "global_sentence_id": 675, "edu_l1_label": "EDU_O"}, {"txt": "Lee, D. 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# Cecelia: a multifunctional image analysis toolbox for decoding spatial cellular interactions and behaviour
## Abstract
## Introduction
## Results
### Cecelia as a general-purpose image analysis framework
### Spatial analysis of cellular interactions in complex 3D images using Cecelia
### Quantitative analysis of highly multiplexed 3D images using Cecelia
### Behavioural analysis of immune cell dynamics using Cecelia reveals hidden cell states
### Integration of structural components and cellular flow into live cell quantification using Cecelia
## Discussion
## Methods
### Animals and ethics statement
### Flank scarification, HSV infection and TRITC dye painting
### LCMV infections
### T cell enrichment, labelling and adoptive transfer
### Dye labelling and adoptive transfer
### Confocal microscopy
### Intravital two-photon microscopy
### Statistics and reproducibility
### Image analysis
### Development of Cecelia
### Design and implementation of Cecelia
### Task management in Cecelia
### Installation options
### Running Cecelia with Docker
### Image segmentation and object measurement
### Object storage and access in Cecelia
### Population management in Cecelia
### Population gating in Cecelia
### Cell tracking in Cecelia
### Neighbour detection in Cecelia
### Plotting data in Cecelia
