Please display appropriate scaling information

[rleigh]

Currently, the OME model stores all physical dimensions in µm, and time in s. However, not all images are at a scale which makes these units the most appropriate for display. Examples: electron microscopy at nm or Å scales, and much larger images, for example dissection microscope images at mm or cm scales. I understand there are also much larger scales also in use. The same also applies to time, where we might want to store timeseries at very short timescales (ms/µs) or at longer timescales on the order of days (live cell or tissue imaging can have inter-frame delays of minutes to hours).

It would be a useful aid if the interface could rescale the measurement into the most appropriate unit. A good rule of thumb would be if it's <1 or >1000, then it needs rescaling to the next smaller or larger unit, respectively. Though cm and Å could be special-cased, perhaps. The units could also be selected in a drop-down selector to rescale manually in the case that the auto-rescaling heuristic did not work.

It would be, I think, useful for the OME model itself to have some concept of units rather than hard-coding µm. This makes it much easier to support more unusual types of microscopy data at the large and small extremes, as well as medical imaging data which at the whole-body scale is certainly not useful to have in µm. This would make it much easier to import data from file formats which do have scaling information, since the information can be imported verbatim. Tools like ImageJ also allow setting of arbitrary scales--this has no impact on making measurements, which are made in the selected pixel or physical units.

[jburel]

see #3741 for existing model ticket

[jburel]

• time is already supported in insight for plane info The values are converted into minutes/hours
• added support for pixels size, noticeable for new supported file formats.

Passing to Will to implement in web

[wmoore]

This won't be for 4.4 (or probably 4.1 - major change).

[jburel <j.burel@…>]

(In [4c2ceb1b4cec71a5659696fd5021967d79459360/ome.git] on branch develop) Transform size into various units. (see #8830)

[jburel <j.burel@…>]

(In [bd6fcc475e26969f549a53764e253822c5824135/ome.git] on branch develop) Centralize units symbols to same class (see #8830)

[jburel <j.burel@…>]

(In [af391b93c24178c39c125bed70ff82123c262e31/ome.git] on branch develop) Adjust units in Viewer depending on pixels size (see #8830)

[jburel <j.burel@…>]

(In [d8cb7eeafd619a06c744708249823f7465c0355f/ome.git] on branch develop) Display scale bar according to units (see #8830)

Calculate the size of the scale bar w.r.t. to units.

[jburel <j.burel@…>]

(In [8f95e67c27a836fb11db2d06b312b2366e7a184d/ome.git] on branch develop) Sets the units depending on pixels size (see #8830)