Commit aa2d6ccf authored by Christian Tischer's avatar Christian Tischer

Update image-ethics-and-data-integrity.md

parent 71a54333
...@@ -32,7 +32,7 @@ ...@@ -32,7 +32,7 @@
#### Explore how saving images can change image content #### Explore how saving images can change image content
- Open an image - Open image: calibrated_16bit__cells_eres_noisy.tif
- Inspect its content and take notes of some pixel values and coordinates - Inspect its content and take notes of some pixel values and coordinates
- Save the image in whatever format (e.g. tiff, png, gif, jpeg, ...) - Save the image in whatever format (e.g. tiff, png, gif, jpeg, ...)
- Reopen the image - Reopen the image
...@@ -43,19 +43,17 @@ Repeat above activity ...@@ -43,19 +43,17 @@ Repeat above activity
- testing different formats for saving - testing different formats for saving
- adjusting the image display before saving - adjusting the image display before saving
##### Example data:
- calibrated_16bit__cells_eres_noisy.tif
### Formative Assessments ### Formative Assessments
How can I ensure that image content is preserved during saving? How can I ensure that image content is preserved during saving?
(Please choose one answer)
1. I always use Tiff format, this is safe. 1. I always use Tiff format, this is safe.
2. I always test it by checking pixel values and coordinates before and after saving. 2. I test it by checking pixel values and coordinates before and after saving.
3. 3. I ask my colleagues in the lab, and do what they do.
## Image data presentation
## Image data visualisation
### Concepts ### Concepts
...@@ -74,8 +72,29 @@ How can I ensure that image content is preserved during saving? ...@@ -74,8 +72,29 @@ How can I ensure that image content is preserved during saving?
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### Activities ### Activities
- Open image: xy_calibrated_16bit__nuclear_protein_control.tif
- This image shows a nuclear protein in control cells.
- Open image: xy_calibrated_16bit__nuclear_protein_treated.tif
- 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
### Formative Assessments ### Formative Assessments
What helps to scientifically convey image intensity information to my audience?
(Please select multiple answers)
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. Adjust the LUT to the full bit-depth of the images
6. Don't change the LUT of the images! Keep it as in the raw data.
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