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# Image ethics and data integrity
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### Duration

1.5 hours

### Learn more

- http://www.imagedataintegrity.com/about.html
- http://jcb.rupress.org/content/166/1/11.full

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## Image data saving

### Concepts
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<img src='https://g.gravizo.com/svg?
 digraph G {
    shift [fontcolor=white,color=white];
    image_integrity -> image_content [label="  preserving"];
    image_content -> pixel_values;
    image_content -> pixel_coordinates;
  }
'/>

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<img src='https://g.gravizo.com/svg?
 digraph G {
    shift [fontcolor=white,color=white];
    saving_images -> image_content [label="  can change"];
  }
'/>


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### Activity: Explore image saving can change image content
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- Open image: `calibrated_16bit__cells_eres_noisy.tif`
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- Inspect its content and take notes of some pixel values and coordinates 
- Save the image in whatever format (e.g. tiff, png, gif, jpeg, ...)
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- Reopen the image
- Compare the image content to your notes, did it change?

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Repeat above activity

- testing different formats for saving
- adjusting the image display before saving

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### Formative assessment
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How can I ensure that image content is preserved during saving (one answer)?
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1. I always use Tiff format, this is safe.
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2. I test it by checking pixel values and coordinates before and after saving.
3. I ask my colleagues in the lab, and do what they do.
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## Lookup tables
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### Concepts

<img src='https://g.gravizo.com/svg?
 digraph G {
    shift [fontcolor=white,color=white];
    lookup_table_settings -> image_appearance [label="  change"];
    image_appearance -> scientific_message [label="  changes"];
  }
'/>

<img src='https://g.gravizo.com/svg?
 digraph G {
    shift [fontcolor=white,color=white];
    responsible_scientist -> lookup_table_settings [label="  configures thoughtfully"];
  }
'/>

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### Activity: Quantitative image display
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- Open image: `xy_calibrated_16bit__nuclear_protein_control.tif`
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    - This image shows a nuclear protein in control cells.   
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- Open image: `xy_calibrated_16bit__nuclear_protein_treated.tif`
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    - The cells in this 'treated' image have been subjected to a drug.
- Inspect the images! 
    - Did the drug affect the nuclear protein?
- Adjust the lookup-tables (LUTs) of both images to be the same
- Add the LUT calibration to both images 
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### Formative Assessment
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What helps to scientifically convey image intensity information (multiple answers)?
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1. Use a grayscale LUT whenever possible.
2. Color the images in the color of the fluorophore.
3. Add a LUT calibration bar.
4. Use the same LUT for all images.
5. Always adjust the LUT to the image's full bit-depth.
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6. Never change the LUT of images! Always keep it as in the raw data.
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## 4-D image display

### Concepts


### Activity: ...

- Open image: `xyzt_calibrated_16bit__golgi_bfa.zip`
- Discuss different options how to present this data

### Formative Assessment


## High dynamic range image display

### Concepts

### Activity: Quantitative image display

- Open image: `xyt_calibrated_16bit__golgi_bfa_sum_projection.tif`

### Formative Assessment


## Image background subtraction

### Concepts


<img src='https://g.gravizo.com/svg?
 digraph G {
    shift [fontcolor=white,color=white];
    image_math -> pixel_values [label="  changes"];
    image_math -> scientific_image_content [label="  can distort"];
  }
'/>

### Activity: ...


### Formative Assessment
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