Up to date May contributions to spreadsheet

https://docs.google.com/spreadsheets/d/1WxuXV6P-xPDahiR6OahPvi9CSe7VgvFNqMt72FNF7Hg/edit#gid=2024568755

checklists/image_publishing/2_image_colors_channels.md

@@ -11,7 +11,8 @@
 Add the staining or marker within or beside the relevant image (panel). 
 ```
 ```{tab-item} Links
-TODO
+[Global BioImaging: Using OMERO.figure to add channel labels](https://youtu.be/5OQgB9fWqSI?t=308)
+
 ```
 ````
 ````` 
@@ -20,10 +21,15 @@ TODO
 ````{tab-set}
 ```{tab-item} Description
 Intensity range adjustments should be monitored with the image histogram and done with care: a too wide intensity range results in ‘faded’ images that lack details, while a too narrow intensity range removes data.
-Use a range indicator LUT (e.g. HiLo in Fiji) to highlight pixels where data was removed due to a too narrow intensity range
+Use a range indicator LUT (e.g. HiLo in Fiji) to highlight pixels where data was removed due to a too narrow intensity range.
+
+Plain brightness adjustments mostly increase background or decrease signal, without improving distinction between different objects, structures or intensities. Contrast increases bright and decreases dark intensities and can lead to a better distinguishability of signals. However it also increases perceived intensitie differences and might suggest stronger changes than occurring in reality. Contrast adjustments directly applied on RGB color images changes color tones of stains. Therefore, only the brightness component of a color image should be adjusted in most cases. Signal should not be clipped and intensity cutoff values should be reported for transparency and reproducibility reasons. Data clipping leads to information loss and over- or under-saturation, which both should be avoided to prevent misinterpretation of published images.
 ```
 ```{tab-item} Links
-TODO
+One quick possibility to adjust the contrast of multiple imaghould be compared in one figure can be achieved [as shown here.](https://youtu.be/F6ll37NOgXc?si=liPCwE-PmWGFgM9Y&t=930)
+[Example images](https://drive.google.com/file/d/1w-tlDERcWSMUKXkzuwC2-ppLr0UNx3W2/view?usp=drive_link)
+
+
 ```
 ````
 `````  
@@ -32,9 +38,11 @@ TODO
 ````{tab-set}
 ```{tab-item} Description
 Any adjustments to the image, such as brightness/contrast must be consistent across all images within an experiment, that might be directly compared.
+
+All changes such as contrast, background subtractions, pseudo-coloring etc. need to be kept strictly the same to keep images comparable. The same holds up for the imaging settings before any image editing.
 ```
 ```{tab-item} Links
-TODO
+One quick possibility to adjust the contrast of multiple imaghould be compared in one figure can be achieved [as shown here.](https://youtu.be/F6ll37NOgXc?si=liPCwE-PmWGFgM9Y&t=930)
 ```
 ````
 ````` 
@@ -54,9 +62,24 @@ TODO
 ````{tab-set}
 ```{tab-item} Description
 Grayscale images are often easier to visually distinguish fine detail within than color channels; providing them ensures the reader can see your phenotype to best effect.
+
+For intensity-based images (e.g. fluorescence) the channels relevant for understanding the conclusion and analysis should be displayed best separately as single channels in a gray range (black to white). Sometimes inversion can positively impact visibility.
 ```
 ```{tab-item} Links
-TODO
+Exporting merge images and grayscale images from Fiji and aligning them in Inkscape:
+https://youtu.be/F6ll37NOgXc?si=ot8oPgYVQ9yh8Pwo&t=1504 (25:04-31:50)
+
+Adding grayscale channels in OMERO.figures:
+https://youtu.be/Mty7_382kMM?si=FQmHvPx5xLjbeqPt&t=542 (9:02-13:00)
+
+Sample images - 
+
+SVG:
+https://drive.google.com/file/d/13j5E4RD3Qxh9M08SNdha841p6EpbqIGF/view?usp=drive_link
+
+PNG:
+https://drive.google.com/file/d/1jgVQdd12muB-qErsTFYCJEkMyU3d8-Uu/view?usp=drive_link
+ 
 ```
 ````
 ````` 
@@ -65,9 +88,17 @@ TODO
 ````{tab-set}
 ```{tab-item} Description
 If creating merged images, ensure the LUTs chosen are separable for color-blind readers; online simulations can help you check this.
+
+Maximally merge up to 3 channels in one composite image. Better are 2 only. For 2 channels the best color combination is green/magenta. For 3 channels cyan/magenta/yellow can be used. The latter might lead to optical oversaturation perception and might be negative in case of very bright signal.
+
+Example:
+Pseudo colors can be added to individual channels in Fiji via the >Image >Lookup Tables menu OR via the BioVoxxel Figure Tools LUT Channels Tool plugin. The latter offers a CDV (color deficient vision) test option to check if color combinations are "color-blind" friendly
 ```
 ```{tab-item} Links
-TODO
+Sample results - 
+SVG: https://drive.google.com/file/d/1st1C1xInJlhAYqBMnBuMHkMfqWZsRAoK/view?usp=drive_link
+PNG: https://drive.google.com/file/d/1udtDpD5pyuSJz8AW2RUT4XMBS27tEHb5/view?usp=drive_link
+
 ```
 ````
 `````  
@@ -80,10 +111,19 @@ TODO
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageColors_7.png" height="50px"> &nbsp; Provide intensity scales (calibration bar) for grayscale, color, pseudocolor
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Intensity calibration bars (or scales) should be provided for better interpretablility of intensity values, ranges and distributions. They can also serve to more quantitatively highlight differences seen by eye. Calibration bars are absolutely necessary if multi-pseudo-colors are used to provide the information about the relation between different colors and actual pixel intensities.
+
+Example:
+In Fiji / ImageJ use >Analyze >Tools >Calibration Bar...
+
 ```
 ```{tab-item} Links
-TODO
+Sample results:
+SVG: 
+https://drive.google.com/file/d/1nidSBMY_BU-LEbb7vo3ZiC0BYTdPp6ob/view?usp=drive_link
+
+PNG:
+https://drive.google.com/file/d/1LqyRhEmfdt7sJvMG6kTG3oedkI10IC7E/view?usp=drive_link
 ```
 ````
 ````` 
@@ -99,15 +139,18 @@ TODO
 TODO
 ```
 ```{tab-item} Links
-TODO
+
+https://www.youtube.com/watch?v=JT9mUkEG-C0&ab_channel=Microcourses
+
+
 ```
 ````
 ````` 
 
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageColors_9.png" height="50px"> &nbsp; Gamma adjustments: additionally provide linear-adjusted image for comparison
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Gamma as well as other non-linear adjustments change relative pixel intensity and color relations and can negatively influence optical intensity comparisons. Overenhancement of specific regions can also occur. Therefore, those changes need to be reported and the original images should be provided for transparency.
 ```
 ```{tab-item} Links
 TODO

checklists/image_publishing/3_image_annotation.md

@@ -7,18 +7,26 @@
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageAnnot_1.png" height="50px"> &nbsp; Add scale information (scale bar, image length; in figure/figure legend)
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Include scale information by incorporating a scale bar within the image to provide a reference for size and distance. Additionally, specify the actual dimensions that the scale bar represents in the figure legend or accompanying text to ensure accurate interpretation of the image's scale.
 ```
 ```{tab-item} Links
-TODO
+Add a scale bar in OMERO Figures:
+https://youtu.be/YeCFaB7VAAQ?si=zui5kBNJZNEQYIPn&t=95
+
+
+Using ImageJ to add a scale bar to an image
+https://www.youtube.com/watch?v=1GVBIEwvfng (2:50)
+
+How to add Scale Bar to an image using ImageJ Software
+https://www.youtube.com/watch?v=o7JE_N-xWZM (3:33)
 ```
 ````
 ````` 
 
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageAnnot_2.png" height="50px"> &nbsp; Explain all annotations (in figure/figure legend)
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Explain all annotations by clearly defining each label, symbol, and color used directly within the figure or in the figure legend. Ensure the figure legend provides comprehensive descriptions to help readers understand the significance and context of each annotation in the image.
 ```
 ```{tab-item} Links
 TODO
@@ -29,18 +37,18 @@ TODO
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageAnnot_3.png" height="50px"> &nbsp; Annotations should be legible (line width, size/point size, color)
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Annotations should be legible by using an appropriate line width, font size, and point size that ensures clarity and readability. Additionally, choose colors that provide strong contrast against the background and other elements in the image to enhance visibility.
 ```
 ```{tab-item} Links
-TODO
+https://postacquisition.wordpress.com/2016/02/01/annotating-images/
 ```
 ````
 ````` 
  
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageAnnot_4.png" height="50px"> &nbsp; Annotations should not obscure key data
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Annotations should be placed thoughtfully to avoid covering or obscuring key data and important features within the image. Ensure that all annotations are positioned in a way that maintains the integrity and clarity of the underlying data, allowing for accurate interpretation.
 ```
 ```{tab-item} Links
 TODO
@@ -57,7 +65,9 @@ TODO
 
 ````{tab-set}
 ```{tab-item} Description
-(Depending on the main message and imaging technique this may be e.g. image pixel size, imaging intervals (time-lapse in movies), exposure time, or anatomical section.)
+Annotate imaging details critical for interpreting the figure, such as the type of microscope used, magnification levels, and staining methods. Additionally, include information on image acquisition settings like exposure time, resolution, and any post-processing techniques applied.
+
+Depending on the main message and imaging technique this may be e.g. image pixel size, imaging intervals (time-lapse in movies), exposure time, or anatomical section.
 ```
 ```{tab-item} Links
 TODO

checklists/image_publishing/4_image_availability.md

@@ -7,10 +7,13 @@
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageAvail_1.png" height="50px"> &nbsp; Images are shared (lossless compression/microscope images)
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Share microscopy images by uploading them to a reputable open-access repository ensuring they are properly annotated with metadata and accompanied by the relevant publication information. Additionally, provide clear licensing terms and link to the repository in the publication and related communications to facilitate easy access for other researchers.
 ```
 ```{tab-item} Links
-TODO
+[Sharing and reusing cell image data - PMC](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5994892/)
+
+Pictures at an exhibition: How to share your imaging data
+https://onlinelibrary.wiley.com/doi/10.1111/jmi.13221
 ```
 ````
 ````` 
@@ -23,7 +26,7 @@ TODO
 `````{dropdown} <img src="/image_publishing/icons_image_publishing/ImageAvail_2.png" height="50px"> &nbsp; Images are freely downloadable (public databse)
 ````{tab-set}
 ```{tab-item} Description
-TODO
+Ensure that image files are made freely downloadable by hosting them on an open-access platform or repository. Provide direct download links and ensure there are no access restrictions, so that other researchers can easily obtain and utilize the images.
 ```
 ```{tab-item} Links
 TODO