A mouse brain atlas using OMERO is out

[Kouichi_C_Nakamura]

Dear OMERO users,

We are delighted to report the launch of CHAMBER (CHemoarchitectonic Atlas of the Mouse thalamus as a BNDU OpEn Resource) at MRC Brain Network Dynamics Unit, Oxford University. This is an example of OMERO use case.

https://data.mrc.ox.ac.uk/chamber

We're aware that we still have a couple of technical issues that need to be fixed or improved and I will post a few questions in the forum soon.

Your feedback will be appreciated!

[img]kms024_s13v4_076%20L+0.jpg[/img]

Best,
Kouichi C. Nakamura

[wmoore]

Hi,
Apologies we didn't reply sooner. This just got flagged up by the team, so I thought I'd reply.

This looks great! Good to see that OMERO and iviewer are working for you.

I noticed that you are using an older version of iviewer, mostly because the thumbnails on the left still need a click on the down-arrow to load more. In iviewer 0.6.0 this was improved to load thumbnails automatically when you scroll the panel.

As you're probably aware, we just released iviewer 0.7.0, which has nicer scalebar display, and you can get a link to your current viewport (x, y, zoom & rendering settings) which you may find useful.

I noticed the "BirdsEye" thumbnail is taking a long time to load, which should be helped by https://github.com/ome/omero-iviewer/pull/260 (not released yet).

I like the Dark theme that you've done. I hope it wasn't too painful and is not too tricky to maintain when you upgrade iviewer.

We were actually discussing your usage of labels the other day. I was wondering whether you like the current behaviour of labels staying a fixed height on the image, and zooming with the image, so that they appear very small when you zoom out and quite big when you zoom in? The alternative is what most on-line maps do: keep a constant size of text with respect to the screen (not the image). The only tricky issue then is how to filter out less important labels when you zoom out (as happens on maps) so that the image is not overwhelmed by too many labels.

Regards,

Will.

[Kouichi_C_Nakamura]

Hi Will,

Thank you for the comment. I'm glad you like our CHAMBER.

We're aware of iviewer 0.7.0, which solved a few issues that I reported in this forum. We'll soon update iviewer and are looking forward to it.

> I like the Dark theme that you've done.

For fluorescent images, dark background is important.

Probably, you can think of preparing light and dark themes for the release, so users can select one.

> I was wondering whether you like the current behaviour of labels staying a fixed height on the image, and zooming with the image, so that they appear very small when you zoom out and quite big when you zoom in? The alternative is what most on-line maps do: keep a constant size of text with respect to the screen (not the image). The only tricky issue then is how to filter out less important labels when you zoom out (as happens on maps) so that the image is not overwhelmed by too many labels.

So far I haven't heard negative feedback about text label size changes. I don't feel stressed about it, perhaps because we're used to see the printed version of brain atlas, in which the size of the font does not adapt.

Making another option might be good.

As to the issue of "how to filter out less important labels when you zoom out (as happens on maps) so that the image is not overwhelmed by too many labels," I guess in the real map situation, you can refer to the population size of cities to prioritize them. For microscopic images, such a reference is not possible, so I guess you may want to introduce an additional field (eg. "SignificanceWeight") to the object to store sorting key as a positive number. By default, the object IDs are to be used. But you can specify the sorting order for all or some of the text objects by specifying numbers.

This sorting key should be separate from the sorting key on the ROI panel on the right. For the ROI panel, the comment values can be used by default, but you can customize the order by assigning values to a dedicated field (eg. "SortingKey").
viewtopic.php?f=4&t=8643

What do you think?

[wmoore]

I created a card for "Dark theme" at https://trello.com/c/MiwEwwsE/77-dark-theme

Certainly, whether to support the non-zooming of labels (and how to filter out 'less important') labels needs some more thought. One possibility is that you could use the font-size of labels as a way to determine importance. E.g. all the smaller font-size labels get filtered out first as you zoom out.
But since you haven't found the current behaviour to be problematic and we don't have feedback from other users, we probably won't try do this anytime soon. Also the switch to non-zooming labels would be a breaking change (unless we supported both, which would need an option to save the change) so a big change.

Thanks for the reminder about sorting ROIs by label text. I was away during that discussion so it's useful to have it flagged up.

Regards,

Will.

[Kouichi_C_Nakamura]

Thanks, I'm sure a lot of people love an option of dark theme!

I agree that the behaviour of labels isn't urgent, though it's worthwhile pursuing.