Extracting the Meaning: Painless processing and analysis of image data with Fiji and Ruby

Extracting the Meaning: Painless processing and analysis of image data with Fiji and Ruby

707d0934f77fc31048f004103e10c57f?s=128

Greg Goltsov

October 23, 2012
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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
  2. 2.

    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
  3. 3.

    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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    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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    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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    RENAMER <id> <desc> <conc> <well> <time> 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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    RENAMER <id> <desc> <conc> <well> <time> 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 396 3uM 1 0h 403 (cont) 1 0h 409 (cont) 4 0h 616 (inact) 30uM 2 0h 403 (cont) 1 24h S4 1uM 1 24h 616 (inact) 1uM 1 48h S4 3uM 4 48h
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    Pseudo Flat-Field correction # Code: # This is the kernel

    size for Gaussian blur. # Smaller kernel removes more background kernel_size = 100 pffc = Computations.pffc imp, kernel_size, true
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    D ≃ 1 Untreated Treated (1μM 396) D ≃ 1.3

    D ≃ 1.32 D ≃ 1 D ≃ 1.15
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    D ≃ 1 Untreated Treated (1μM 396) D ≃ 1.3

    D ≃ 1.32 D ≃ 1 D ≃ 1.15 D ≃ 1.28
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    thank you! gregory@goltsov.info www.gregory.goltsov.info Questions? melville f o u n

    d a t i o n Big thanks to: School of CONTEMPORARY SCIENCES