figure/Guidelines.md

+# Image Processing Guidelines
+
+The [Office of Research Integrity][ORI] has 4 golden rules:
+
+* **Treat all pixels equally:** No specific feature within an image may be enhanced, obscured, moved, removed, or introduced.
+* **Simple adjustments are OK:** Adjustments of brightness, contrast, or color balance are acceptable if they are applied to the whole image and as long as they do not obscure, eliminate, or misrepresent any information present in the original.
+* **Don't cut or paste** The grouping of images from different parts of the same gel, or from different gels, fields, or exposures must be made explicit by the arrangement of the figure (e.g., dividing lines) and in the text of the figure legend.
+* **Keep the orginals** If the original data cannot be produced by an author when asked to provide it, acceptance of the manuscript may be revoked.
+
+
+
+# More detail
+## Generally acceptable
+##### Cropping
+Usually OK. Don't present only the 'best' cells though.  
+
+
+##### Brightness and contrast changes
+Are usually OK, don't hide information by truncating the histogram.
+
+##### Gamma
+Allows intensity range to compressed or expanded.  Must  be reported.
+
+## Unacceptable
+
+Adding / removing content from the image
+
+* Pasting from other image (without making an inset) 
+* Deleting regions
+* Clone stamp
+* Content aware fill
+
+Filters that treat parts of image differently
+
+* 'Healing' tool
+* Edge enhancers
+* Despeckle
+ 
+
+## Specific guidelines
+
+* Fluorescence images should show signals from individual channels in gray scale to reveal the full dynamic range of intensities. Merged images should be presented in color, with distinct colors for individual channels. [JBC]
+![](media/channel_comp.png)
+
+* For primary antibody and secondary antibody combinations, controls such as a non-immune antibody, omission of the primary antibody, and absence of antigen may be necessary to demonstrate specificity. [JBC]
+* Do not prepare images in PowerPoint or save them in JPEG format.
+* If you are using the same the control in two figures clearly state this in the figure legend.
+
+
+## Intensity measurements
+
+When comparing intensity measurements:
+
+* All images must be taken under identical settings (lamp power, filters, exposure etc)
+* All images must be processed the same way
+* Ideally images acquired in the same session.
+
+## Reporting
+
+* type of microscope, 
+* objective lenses, cameras
+* camera / detectors
+* fluorophore excitation and emission wavelengths or ranges
+* details of the light sources, filters and beamsplitters 
+* Name of the acquisition software program and version number
+* Name of the processing software program and version number
+* Name of tool / plugins within that program and their mportant settings.
+
+#### From [Nature]:
+A single Supplementary Methods file (or part of a larger Methods section) titled "Equipment and Settings" should list for each image: 
+
+* acquisition information, 
+* time and space resolution data (xyzt and pixel dimensions)
+* image bit depth
+* experimental conditions such as temperature and imaging medium;
+*  fluorochromes excitation and emission wavelengths or ranges 
+*  filters, dichroic beamsplitters.
+
+Images gathered at different times or from different locations should not be combined into a single image, unless it is stated that the resultant image is a product of time-averaged data or a time-lapse sequence. If juxtaposing images is essential, the borders should be clearly demarcated in the figure and described in the legend.
+
+
+
+[Nature]: https://www.nature.com/authors/policies/image.html
+[ORI]: https://ori.hhs.gov/education/products/RIandImages/guidelines/list.html
+[JBC]:http://jbcresources.asbmb.org/collecting-and-presenting-data
+[1]:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114110/