painless processing and analysis of
image data with Fiji and Ruby
extracting the meaning
Based on the experience from the
summer project by Gregory Goltsov
melville
f o u n d a t i o n
Supervisor
Dr Anne Savage
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painless processing and analysis of
image data with Fiji and Ruby
extracting the meaning
Based on the experience from the
summer project by Gregory Goltsov
melville
f o u n d a t i o n
Supervisor
Dr Anne Savage
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painless processing and analysis of
image data with Fiji and Ruby
extracting the meaning
Based on the experience from the
summer project by Gregory Goltsov
melville
f o u n d a t i o n
Supervisor
Dr Anne Savage
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who am i?
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who am i?
4th year Computer
Games Technology
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who am i?
4th year Computer
Games Technology
Ruby fan
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who am i?
4th year Computer
Games Technology
Ruby fan
(basically) a
programmer
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the project
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No content
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Data
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Breakthrough Breast Cancer Research Unit and Division of Pathology,
University of Edinburgh
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Breakthrough Breast Cancer Research Unit and Division of Pathology,
University of Edinburgh
Breast
cancer
spheroid
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Breakthrough Breast Cancer Research Unit and Division of Pathology,
University of Edinburgh
Breast
cancer
spheroid
Drug
396
403
S4
...
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Breakthrough Breast Cancer Research Unit and Division of Pathology,
University of Edinburgh
Breast
cancer
spheroid
Drug
396
403
S4
...
?
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Breakthrough Breast Cancer Research Unit and Division of Pathology,
University of Edinburgh
Aim
To develop a metric to
objectively measure the
effectiveness of said drugs
on the spheroids
Breast
cancer
spheroid
Drug
396
403
S4
...
?
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Data
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Data
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pre-processing • processing • analysis
Data
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pre-processing • processing • analysis
Data
Results
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pre-processing • processing • analysis
Data
Results
──────
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pre-processing • processing • analysis
Data
Results
──────
Scalable
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pre-processing • processing • analysis
Data
Results
──────
Scalable
Robust
pre-processing • processing • analysis
Filtering invalid data
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pre-processing • processing • analysis
Filtering invalid data
Renaming
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396 3um well1 time0
403Contwell1time0
409BCont4time0
616inact 30um well2 time0
403 Cont 1 24h
S4 1uM 1 24h
616 (inact) 1uM 1 time 48h
S4 3 uM 4a time 48h
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396 3um well1 time0
403Contwell1time0
409BCont4time0
616inact 30um well2 time0
403 Cont 1 24h
S4 1uM 1 24h
616 (inact) 1uM 1 time 48h
S4 3 uM 4a time 48h
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396 3um well1 time0
403Contwell1time0
409BCont4time0
616inact 30um well2 time0
403 Cont 1 24h
S4 1uM 1 24h
616 (inact) 1uM 1 time 48h
S4 3 uM 4a time 48h
How to retrieve a
particular image?
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396 3um well1 time0
403Contwell1time0
409BCont4time0
616inact 30um well2 time0
403 Cont 1 24h
S4 1uM 1 24h
616 (inact) 1uM 1 time 48h
S4 3 uM 4a time 48h
How to retrieve a
particular image?
W
hat is the id?
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396 3um well1 time0
403Contwell1time0
409BCont4time0
616inact 30um well2 time0
403 Cont 1 24h
S4 1uM 1 24h
616 (inact) 1uM 1 time 48h
S4 3 uM 4a time 48h
How to retrieve a
particular image?
W
hat is the id?
What is the drug
concentration?
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396 3um well1 time0
403Contwell1time0
409BCont4time0
616inact 30um well2 time0
403 Cont 1 24h
S4 1uM 1 24h
616 (inact) 1uM 1 time 48h
S4 3 uM 4a time 48h
How to retrieve a
particular image?
W
hat is the id?
What is the drug
concentration?
Can these be put
into a database?
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So I implemented the
RENAMER
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RENAMER
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RENAMER
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RENAMER
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RENAMER
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But why bother with
RENAMER ?
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But why bother with
RENAMER ?
Consistent
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But why bother with
RENAMER ?
Consistent Scalable
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But why bother with
RENAMER ?
Consistent Scalable DB-like querying
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But why bother with
RENAMER ?
Consistent
Time-series analysis
Scalable DB-like querying
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But why bother with
RENAMER ?
Consistent
Time-series analysis
Robust
Scalable DB-like querying