High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
Freiburg im Breisgau
March 2023
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Beschreibung: | Enthält Sonderabdrucke |
| Beschreibung: | 230 Seiten Illustrationen, Diagramme 30 cm |
Internformat
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| 245 | 1 | 0 | |a High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |c submitted by Mischa Selig |
| 264 | 1 | |a Freiburg im Breisgau |c March 2023 | |
| 300 | |a 230 Seiten |b Illustrationen, Diagramme |c 30 cm | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 500 | |a Enthält Sonderabdrucke | ||
| 502 | |b Dissertation |c Albert-Ludwigs-University Freiburg |d 2023 | ||
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 710 | 2 | |a Albert-Ludwigs-Universität Freiburg |0 (DE-588)2024338-8 |4 dgg | |
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Datensatz im Suchindex
| _version_ | 1804186458649526272 |
|---|---|
| adam_text | TABLE
OF
CONTENTS
ABSTRACT
.............................................................................................................................
1
ZUSAMMENFASSUNG
............................................................................................................
4
ACKNOWLEDGMENTS
.............................................................................................................
8
LIST
OF
TABLES
...................................................................................................................
13
LIST
OF
FIGURES
..................................................................................................................
13
LIST
OF
ALL
PUBLICATIONS
BY
THE
AUTHOR
.............................................................................
14
PEER-REVIEWED
SCIENTIFIC
PUBLICATIONS:
..........................................................................
14
PEER-REVIEWED
SCIENTIFIC
REVIEWS:.................................................................................
14
UNPUBLISHED
MANUSCRIPTS
OF
THIS
THESIS:
.......................................................................
15
CHAPTER
1:
INTRODUCTION
...................................................................................................
16
1.1
MOTIVATION
FOR
THIS
THESIS
.........................................................................................
16
1.2
GENERAL
CARTILAGE
AND
CHONDROCYTE
BIOLOGY
............................................................
17
1.3
SPATIAL
ORGANIZATION
OF
CHONDROCYTES
AT
THE
ARTICULAR
SURFACE
................................
18
1.4
IMAGE-BASED
SINGLE
CELLULAR
PHENOTYPING
................................................................
20
1.5
SINGLE-CELL
SEGMENTATION
.........................................................................................
21
CHAPTER
2:
HIGH-THROUGHPUT
IMAGE
AND
DATA
ANALYSIS
.................................................
22
2.1
IMAGE
ANALYSIS
BACKGROUND
INFORMATION
.................................................................
22
STEP
1:
PRE-PROCESSING
OF
THE
IMAGE
..............................................................................................
23
STEP
2:
OBJECT
SEGMENTATION
..........................................................................................................
23
STEP
3:
FEATURE
EXTRACTION
FOR
OBJECT
PROFILING
................................................................................
24
2.2
SPATIAL
ANALYSIS
OF
CHONDROCYTES
IN
THE
AC
TISSUE
...................................................
25
9
2.3
SINGLE-CELL
MORPHOLOGY
............................................................................................
27
2.4
SINGLE-CELL
PROTEIN
EXPRESSION
.................................................................................
28
2.5
SINGLE-CELL
STRESS
FIBER
CHARACTERISTICS
....................................................................
28
CHAPTER
3:
CONCEPTS
OF
MACHINE
LEARNING
......................................................................
30
3.1
FUNDAMENTAL
MACHINE
LEARNING
CONCEPTS
...............................................................
30
3.2
MACHINE
LEARNING
CLASSIFICATION
...............................................................................
32
3.2.1
EVALUATION
AND
PERFORMANCE
METRICS
OF
MACHINE
LEARNING
CLASSIFICATION
............
32
3.3
REGRESSION
ALGORITHMS
.............................................................................................
33
3.3.1
EVALUATION
AND
PERFORMANCE
METRICS
OF
MACHINE
LEARNING
REGRESSION
...................................
34
3.3
TECHNIQUES
TO
UNDERSTAND
AND
IMPROVE
ALGORITHM
PERFORMANCE
.............................
34
3.3.1
CROSS-VALIDATION
.....................................................................................................................
34
3.3.2
FEATURE
IMPORTANCE
................................................................................................................
35
3.4
EXAMPLES
OF
MACHINE
LEARNING
ALGORITHMS
..............................................................
36
3.4.1
DECISION
TREES
........................................................................................................................
36
3.4.2
RANDOM
FOREST
......................................................................................................................
36
3.5
PARTIAL
LEAST-SQUARES
DISCRIMINANT
ANALYSIS
...........................................................
37
CHAPTER
4:
AN
AUTOMATED,
SEMI-USER-INDEPENDENT
CELL
SEGMENTATION
TOOL
FOR
SINGLE-CELL
ANALYSIS
IN
COMPLEX
BIOLOGICAL
SITUATIONS
......................................................................
39
4.1
INTRODUCTION
............................................................................................................
39
4.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
........................................................
40
4.3
PUBLICATION
OVERVIEW
AND
SUMMARY
........................................................................
40
4.4
CONCLUSION
..............................................................................................................
41
CHAPTER
5:
CELL
MORPHOLOGY
AS
A
BIOLOGICAL
FINGERPRINT
OF
CHONDROCYTE
PHENOTYPE
IN
CONTROL
AND
INFLAMMATORY
CONDITIONS
.............................................................................
74
5.1
INTRODUCTION
............................................................................................................
74
10
5.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.........................................................
76
5.3
PUBLICATION
OVERVIEW
AND
SUMMARY
...................
77
5.4
DISCUSSION
..............................................................................................................
78
CHAPTER
6:
ESTABLISHING
A
PHENOTYPIC
CLASSIFICATION
PROFILE
OF
IL-1
P
TREATED
CHONDROCYTES
BASED
ON
SINGLE
CELL
MORPHOLOGY,
PROTEIN
EXPRESSION,
AND
F-ACTIN
STRESS
FIBER
CHARACTERISTICS
.......................................................................................................
101
6.1
INTRODUCTION
...........................................................................................................
101
6.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
..................................................
.....103
6.3
PUBLICATION
OVERVIEW
AND
SUMMARY
......................................................................
104
6.4
DISCUSSION
............................................................................................................
105
CHAPTER
7:
PROOF-OF-CONCEPT
FOR
THE
DETECTION
OF
EARLY
OA
PATHOLOGY
BY
CLINICALLY
APPLICABLE
ENDOMICROSCOPY
AND
QUANTITATIVE
AL-SUPPORTED
OPTICAL
BIOPSY
.................
142
7.1
INTRODUCTION
...........................................................................................................
142
7.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.......................................................
143
7.3
PUBLICATION
OVERVIEW
AND
SUMMARY
.....................................................................
144
7.4
DISCUSSION
..........................................................................................................
145
CHAPTER
8:
USING
A
MACHINE
LEARNING-SUPPORTED
APPROACH
FOR
ASSESSING
AND
PREDICTING
ARTICULAR
CARTILAGE
SURFACE
STRUCTURE
DAMAGE
AND
ITS
SUSCEPTIBILITY
TO
MECHANICAL
TRAUMA-INDUCED
CHANGES
IN
CELLULARITY
..........................................................................
158
8.1
INTRODUCTION
...........................................................................................................
158
8.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.......................................................
160
8.3
PUBLICATION
OVERVIEW
AND
SUMMARY
......................................................................
161
8.4
DISCUSSION
............................................................................................................
162
CHAPTER
9:
OUTLOOK
........................................................................................................
208
11
CHAPTER
10:
SUMMARY
....................................................................................................
211
LIST
OF
ABBREVIATIONS
....................................................................................................
215
12
|
| adam_txt |
TABLE
OF
CONTENTS
ABSTRACT
.
1
ZUSAMMENFASSUNG
.
4
ACKNOWLEDGMENTS
.
8
LIST
OF
TABLES
.
13
LIST
OF
FIGURES
.
13
LIST
OF
ALL
PUBLICATIONS
BY
THE
AUTHOR
.
14
PEER-REVIEWED
SCIENTIFIC
PUBLICATIONS:
.
14
PEER-REVIEWED
SCIENTIFIC
REVIEWS:.
14
UNPUBLISHED
MANUSCRIPTS
OF
THIS
THESIS:
.
15
CHAPTER
1:
INTRODUCTION
.
16
1.1
MOTIVATION
FOR
THIS
THESIS
.
16
1.2
GENERAL
CARTILAGE
AND
CHONDROCYTE
BIOLOGY
.
17
1.3
SPATIAL
ORGANIZATION
OF
CHONDROCYTES
AT
THE
ARTICULAR
SURFACE
.
18
1.4
IMAGE-BASED
SINGLE
CELLULAR
PHENOTYPING
.
20
1.5
SINGLE-CELL
SEGMENTATION
.
21
CHAPTER
2:
HIGH-THROUGHPUT
IMAGE
AND
DATA
ANALYSIS
.
22
2.1
IMAGE
ANALYSIS
BACKGROUND
INFORMATION
.
22
STEP
1:
PRE-PROCESSING
OF
THE
IMAGE
.
23
STEP
2:
OBJECT
SEGMENTATION
.
23
STEP
3:
FEATURE
EXTRACTION
FOR
OBJECT
PROFILING
.
24
2.2
SPATIAL
ANALYSIS
OF
CHONDROCYTES
IN
THE
AC
TISSUE
.
25
9
2.3
SINGLE-CELL
MORPHOLOGY
.
27
2.4
SINGLE-CELL
PROTEIN
EXPRESSION
.
28
2.5
SINGLE-CELL
STRESS
FIBER
CHARACTERISTICS
.
28
CHAPTER
3:
CONCEPTS
OF
MACHINE
LEARNING
.
30
3.1
FUNDAMENTAL
MACHINE
LEARNING
CONCEPTS
.
30
3.2
MACHINE
LEARNING
CLASSIFICATION
.
32
3.2.1
EVALUATION
AND
PERFORMANCE
METRICS
OF
MACHINE
LEARNING
CLASSIFICATION
.
32
3.3
REGRESSION
ALGORITHMS
.
33
3.3.1
EVALUATION
AND
PERFORMANCE
METRICS
OF
MACHINE
LEARNING
REGRESSION
.
34
3.3
TECHNIQUES
TO
UNDERSTAND
AND
IMPROVE
ALGORITHM
PERFORMANCE
.
34
3.3.1
CROSS-VALIDATION
.
34
3.3.2
FEATURE
IMPORTANCE
.
35
3.4
EXAMPLES
OF
MACHINE
LEARNING
ALGORITHMS
.
36
3.4.1
DECISION
TREES
.
36
3.4.2
RANDOM
FOREST
.
36
3.5
PARTIAL
LEAST-SQUARES
DISCRIMINANT
ANALYSIS
.
37
CHAPTER
4:
AN
AUTOMATED,
SEMI-USER-INDEPENDENT
CELL
SEGMENTATION
TOOL
FOR
SINGLE-CELL
ANALYSIS
IN
COMPLEX
BIOLOGICAL
SITUATIONS
.
39
4.1
INTRODUCTION
.
39
4.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.
40
4.3
PUBLICATION
OVERVIEW
AND
SUMMARY
.
40
4.4
CONCLUSION
.
41
CHAPTER
5:
CELL
MORPHOLOGY
AS
A
BIOLOGICAL
FINGERPRINT
OF
CHONDROCYTE
PHENOTYPE
IN
CONTROL
AND
INFLAMMATORY
CONDITIONS
.
74
5.1
INTRODUCTION
.
74
10
5.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.
76
5.3
PUBLICATION
OVERVIEW
AND
SUMMARY
.
77
5.4
DISCUSSION
.
78
CHAPTER
6:
ESTABLISHING
A
PHENOTYPIC
CLASSIFICATION
PROFILE
OF
IL-1
P
TREATED
CHONDROCYTES
BASED
ON
SINGLE
CELL
MORPHOLOGY,
PROTEIN
EXPRESSION,
AND
F-ACTIN
STRESS
FIBER
CHARACTERISTICS
.
101
6.1
INTRODUCTION
.
101
6.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.
.103
6.3
PUBLICATION
OVERVIEW
AND
SUMMARY
.
104
6.4
DISCUSSION
.
105
CHAPTER
7:
PROOF-OF-CONCEPT
FOR
THE
DETECTION
OF
EARLY
OA
PATHOLOGY
BY
CLINICALLY
APPLICABLE
ENDOMICROSCOPY
AND
QUANTITATIVE
AL-SUPPORTED
OPTICAL
BIOPSY
.
142
7.1
INTRODUCTION
.
142
7.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.
143
7.3
PUBLICATION
OVERVIEW
AND
SUMMARY
.
144
7.4
DISCUSSION
.
145
CHAPTER
8:
USING
A
MACHINE
LEARNING-SUPPORTED
APPROACH
FOR
ASSESSING
AND
PREDICTING
ARTICULAR
CARTILAGE
SURFACE
STRUCTURE
DAMAGE
AND
ITS
SUSCEPTIBILITY
TO
MECHANICAL
TRAUMA-INDUCED
CHANGES
IN
CELLULARITY
.
158
8.1
INTRODUCTION
.
158
8.2
CONTRIBUTIONS
OF
THE
AUTHOR
TO
THE
PUBLICATION
.
160
8.3
PUBLICATION
OVERVIEW
AND
SUMMARY
.
161
8.4
DISCUSSION
.
162
CHAPTER
9:
OUTLOOK
.
208
11
CHAPTER
10:
SUMMARY
.
211
LIST
OF
ABBREVIATIONS
.
215
12 |
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| any_adam_object_boolean | 1 |
| author | Selig, Mischa |
| author_GND | (DE-588)121617878X |
| author_facet | Selig, Mischa |
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| author_sort | Selig, Mischa |
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| building | Verbundindex |
| bvnumber | BV049588535 |
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| genre | (DE-588)4113937-9 Hochschulschrift gnd-content |
| genre_facet | Hochschulschrift |
| id | DE-604.BV049588535 |
| illustrated | Illustrated |
| index_date | 2024-07-03T23:33:00Z |
| indexdate | 2024-07-10T10:11:27Z |
| institution | BVB |
| institution_GND | (DE-588)2024338-8 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-034933263 |
| oclc_num | 1393206879 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR |
| owner_facet | DE-355 DE-BY-UBR |
| physical | 230 Seiten Illustrationen, Diagramme 30 cm |
| publishDate | 2023 |
| publishDateSearch | 2023 |
| publishDateSort | 2023 |
| record_format | marc |
| spelling | Selig, Mischa Verfasser (DE-588)121617878X aut High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis submitted by Mischa Selig Freiburg im Breisgau March 2023 230 Seiten Illustrationen, Diagramme 30 cm txt rdacontent n rdamedia nc rdacarrier Enthält Sonderabdrucke Dissertation Albert-Ludwigs-University Freiburg 2023 (DE-588)4113937-9 Hochschulschrift gnd-content Albert-Ludwigs-Universität Freiburg (DE-588)2024338-8 dgg B:DE-101 application/pdf https://d-nb.info/1303866110/04 Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034933263&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis 1\p dnb 20231215 DE-101 https://d-nb.info/provenance/plan#dnb 2\p dnb 20231215 DE-101 https://d-nb.info/provenance/plan#dnb 3\p dnb 20231215 DE-101 https://d-nb.info/provenance/plan#dnb |
| spellingShingle | Selig, Mischa High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| subject_GND | (DE-588)4113937-9 |
| title | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| title_auth | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| title_exact_search | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| title_exact_search_txtP | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| title_full | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis submitted by Mischa Selig |
| title_fullStr | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis submitted by Mischa Selig |
| title_full_unstemmed | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis submitted by Mischa Selig |
| title_short | High-throughput machine-learning-supported image-based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| title_sort | high throughput machine learning supported image based phenotyping of single chondrocytes and articular cartilage tissues for diagnosis |
| topic_facet | Hochschulschrift |
| url | https://d-nb.info/1303866110/04 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=034933263&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT seligmischa highthroughputmachinelearningsupportedimagebasedphenotypingofsinglechondrocytesandarticularcartilagetissuesfordiagnosis AT albertludwigsuniversitatfreiburg highthroughputmachinelearningsupportedimagebasedphenotypingofsinglechondrocytesandarticularcartilagetissuesfordiagnosis |
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