Commit a0cd6918 authored by Christian Tischer's avatar Christian Tischer

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

parent f42a00d5
......@@ -9,7 +9,9 @@
- http://www.imagedataintegrity.com/about.html
- http://jcb.rupress.org/content/166/1/11.full
## Image data integrity
## Image data saving
### Concepts
<img src='https://g.gravizo.com/svg?
digraph G {
......@@ -28,11 +30,9 @@
'/>
### Activities
#### Explore how saving images can change image content
### Activity: Explore image saving can change image content
- Open image: calibrated_16bit__cells_eres_noisy.tif
- Open image: `calibrated_16bit__cells_eres_noisy.tif`
- Inspect its content and take notes of some pixel values and coordinates
- Save the image in whatever format (e.g. tiff, png, gif, jpeg, ...)
- Reopen the image
......@@ -43,7 +43,7 @@ Repeat above activity
- testing different formats for saving
- adjusting the image display before saving
### Formative assessments
### Formative assessment
How can I ensure that image content is preserved during saving (one answer)?
......@@ -52,7 +52,7 @@ How can I ensure that image content is preserved during saving (one answer)?
3. I ask my colleagues in the lab, and do what they do.
## Image data visualisation
## Lookup tables
### Concepts
......@@ -72,23 +72,18 @@ How can I ensure that image content is preserved during saving (one answer)?
'/>
### Activities
### Activity: Quantitative image display
#### Comparing images
- Open image: xy_calibrated_16bit__nuclear_protein_control.tif
- 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
- 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
#### Adjusting the LUT for high dynamic range images
### Formative Assessments
### Formative Assessment
What helps to scientifically convey image intensity information (multiple answers)?
......@@ -99,5 +94,46 @@ What helps to scientifically convey image intensity information (multiple answer
5. Always adjust the LUT to the image's full bit-depth.
6. Never change the LUT of images! Always keep it as in the raw data.
## 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
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment