IGV for Apple systems really needs a dark mode

[Sam8138]

IGV for Apple systems really needs a dark mode. Ideal would be for the app to follow the systems setting for that. Second best would be app settings to change the theme and to be able to customize that. The age of stroke bright white with black text is long over.

LED blue light (heavily present in "white" from LED screens -> all of them now) is intensely damaging to the retina, and when exposure occurs after sundown causes suppression of melatonin and breakdown of the bodies circadian rhythm leading to all sorts of diseases skyrocketing. Both the blue damaging the retina, and the melatonin suppression lead to myriad diseases and maladies including obesity, cardiovascular disease, type II diabetes, breast cancer, prostate cancer, GI and rectal cancer, depression, suicide, macular degeneration, blindness, and worse.

It is possible to adjust the colors in browser versions through igv.js and css. It is not easily possible to alter the java code for the apps without knowing a whole lot more code than I or most people ever want to learn. This needs to be a deep system level change to enable the feature easily for users on all platforms.

I would go further and argue that the default should be dark mode.

[jrobinso]

In the next major release of IGV, available now in the development build, you can select a dark mode look & feel. The problem however is the large number of tracks with light backgrounds. They need redesigned individually, including all the feature color settings. Alignments can probably not be represented by a dark gray rectangle for example. Its a large development task for a small team and will take significant time.

You will have the same issue with igv.js, or any genome browser that I am aware of. You will not be able to effect track colors by simply changing css, it will have the same effect as choosing a look & feel in Java. Menus and UI elements will change but tracks will note.

[maximilianh]

Yes. We have the same problem. I cannot find serious data that white background is actually harmful for the eyes and users are not using genome browsers for hours and hours, like they would use a word processor, I assume, so we treat this as a will-not-fix for now.

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On Tue, May 27, 2025 at 10:39 PM Jim Robinson ***@***.***> wrote: *jrobinso* left a comment (igvteam/igv#1700) <#1700 (comment)> In the next major release of IGV, available now in the development build, you can select a dark mode look & feel. The problem however is the large number of tracks with light backgrounds. They need redesigned individually, including all the feature color settings. Alignments can probably not be represented by a dark gray rectangle for example. Its a large development task for a small team and will take significant time. I'm not aware of any genome browser with a dark mode. You will have the same issue with igv.js, or any genome browser that I am aware of. You will not be able to effect track colors by simply changing css, it will have the same effect as choosing a look & feel in Java. Menus and UI elements will change but tracks will note. — Reply to this email directly, view it on GitHub <#1700 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACL4TOA2TBW5GKBZ5ZEGJL3ATEQVAVCNFSM6AAAAAB6ATFEHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDSMJTHE3TSNJUGU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Sam8138]

Jim -THANK YOU. I along with many others am acutely injured by blue light from LED displays. And sitting anylzing my own genome ---- for hours and hours ---- day after day, it is important.On May 27, 2025, at 1:39 PM, Jim Robinson ***@***.***> wrote:jrobinso left a comment (igvteam/igv#1700) In the next major release of IGV, available now in the development build, you can select a dark mode look & feel. The problem however is the large number of tracks with light backgrounds. They need redesigned individually, including all the feature color settings. Alignments can probably not be represented by a dark gray rectangle for example. Its a large development task for a small team and will take significant time. I'm not aware of any genome browser with a dark mode. You will have the same issue with igv.js, or any genome browser that I am aware of. You will not be able to effect track colors by simply changing css, it will have the same effect as choosing a look & feel in Java. Menus and UI elements will change but tracks will note. —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[Sam8138]

Maximilian, That you have not found such data merely shows that you have not looked, Start your education by looking up a Spanish research paper on the dangers of ALAN (ambient light at night) from 2018. What they studied wasn't just ambient light at night, it was the terrible impacts leading to dramatic increases in breast and prostate cancer caused by the shift to LED street lights in Spain.Next, go back a decade and begin reading the science about the impacts of cell phones, tablets and devices on kids, then on adults, then ....The data is there for any casual researcher to find. Ignorance is not wisdom.For those of us most impacted, the consequences are devastating. And delving through the depths of my genome, yes I have spent hours and hours and days and days staring at that white screen - with nightshift turned to maximum, brightness turned way down and wearing blue blocking glasses. On May 27, 2025, at 2:04 PM, Maximilian Haeussler ***@***.***> wrote:maximilianh left a comment (igvteam/igv#1700) Yes. We have the same problem. I cannot find serious data that white background is actually harmful for the eyes and users are not using genome browsers for hours and hours, like they would use a word processor, I assume, so we treat this as a will-not-fix for now.

On Tue, May 27, 2025 at 10:39 PM Jim Robinson ***@***.***> wrote: *jrobinso* left a comment (igvteam/igv#1700) <#1700 (comment)> In the next major release of IGV, available now in the development build, you can select a dark mode look & feel. The problem however is the large number of tracks with light backgrounds. They need redesigned individually, including all the feature color settings. Alignments can probably not be represented by a dark gray rectangle for example. Its a large development task for a small team and will take significant time. I'm not aware of any genome browser with a dark mode. You will have the same issue with igv.js, or any genome browser that I am aware of. You will not be able to effect track colors by simply changing css, it will have the same effect as choosing a look & feel in Java. Menus and UI elements will change but tracks will note. — Reply to this email directly, view it on GitHub <#1700 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AACL4TOA2TBW5GKBZ5ZEGJL3ATEQVAVCNFSM6AAAAAB6ATFEHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDSMJTHE3TSNJUGU> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you authored the thread.Message ID: ***@***.***>

[jrobinso]

@Sam8138 It looks like JBrowse might have a dark mode https://jbrowse.org/jb2/docs/config_guides/theme/, so you might look into using that. I think the alignment and variant tracks are quite similar to IGV. @cmdcolin might be able to confirm.

@cmdcolin, what does an alignment track look like in dark mode? Is the background black? Do the other colors (alignments, base mismatches, etc,) adjust?

[Sam8138]

I will check it out. Thank you. I downloaded it last night. Though I have not yet had time to 'play' with it.On May 28, 2025, at 11:18 AM, Jim Robinson ***@***.***> wrote:jrobinso left a comment (igvteam/igv#1700) @Sam8138 It looks like JBrowse might have a dark mode https://jbrowse.org/jb2/docs/config_guides/theme/, so you might look into using that. I think the alignment and variant tracks are quite similar to IGV. @cmdcolin might be able to confirm. @cmdcolin, what does an alignment track look like in dark mode? Is the background black? Do the other colors (alignments, base mismatches, etc,) adjust? —Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

[cmdcolin]

thanks for the shout out.

the alignments track colors are pretty much the same in dark and light mode, so it's not super ideal for dark mode...would be nice to adaptively change it better

example screenshot

[jrobinso]

Usable though. The annotation track looks good. Sent from Gmail Mobile

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On Wed, May 28, 2025 at 4:54 PM Colin Diesh ***@***.***> wrote: *cmdcolin* left a comment (igvteam/igv#1700) <#1700 (comment)> thanks for the shout out. the alignments track colors are pretty much the same in dark and light mode, so it's not super ideal for dark mode...would be nice to adaptively change it better example screenshot image.png (view on web) <https://github.com/user-attachments/assets/8eaef08f-2554-4780-8948-dfdf84c1eeb9> — Reply to this email directly, view it on GitHub <#1700 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAHD2HAFIKE2NNDP7IZKD3L3AYPCHAVCNFSM6AAAAAB6ATFEHGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDSMJXGU4DQNZWG4> . You are receiving this because you commented.Message ID: ***@***.***>

[chuddy-ibk]

hey all. I was sent here from the google groups of igv since i also asked for a dark mode there recently:
"..As a visual impaired person, I struggle much with bright background (it hurts my eyes) and small fonts, weak contrast and too similar colors.."
I am using it on Ubuntu :)
Just wanna be up to date on this discussion and I could test versions to see if i can see and differentiate things.
cheers.

[jrobinso]

I am making progress on this.

[jrobinso]

The snapshot build now has a dark mode option. This is the first attempt and we would appreciate feedback. Not every dialog and track type in IGV has been checked, its very possible you will encounter some rather bright screens. Please report these here. Also, some color choices might need refined in dark mode. Color is not always in our control, some tracks specify specific colors in the track data itself.

You can install the snapshot version here: https://igv.org/doc/desktop/#DownloadSnapshot/. Note the instructions if you are on a Mac, you will need to use the generic all-platform version and install Java 21 independently. To enable dark mode select "View > Preferences", then scroll to the bottom, select one of the dark themes ("FLATDARK" or "FLATINTELLIJDARK"), and restart IGV.

Also, note that menus in this version have been redesigned. Tracks are now loaded from the "Tracks" menu.

[chuddy-ibk]

The snapshot build now has a dark mode option. This is the first attempt and we would appreciate feedback. Not every dialog and track type in IGV has been checked, its very possible you will encounter some rather bright screens. Please report these here. Also, some color choices might need refined in dark mode. Color is not always in our control, some tracks specify specific colors in the track data itself.

You can install the snapshot version here: https://igv.org/doc/desktop/#DownloadSnapshot/. Note the instructions if you are on a Mac, you will need to use the generic all-platform version and install Java 21 independently. To enable dark mode select "View > Preferences", then scroll to the bottom, select one of the dark themes ("FLATDARK" or "FLATINTELLIJDARK"), and restart IGV.

Also, note that menus in this version have been redesigned. Tracks are now loaded from the "Tracks" menu.

Hey thank you. Looks already great, i fell in love with this snapshot.
So in the short time i had a look at it I realized following for the flatdark mode on my ubuntu system:

1. when in "preference", i see two "three dot button" next to each other at the very bottom, the left probably "ok" and the right i guess "cancel". Is this normal and expected? The left one worked together with the restart to go into dark mode.
2. I realized that the font is nice and big, but when I pulled a bam file into igv, the name on the left was tiny. I decided to change the font size from 10 to 18 and restarted. Now every font (also the bar at the top) is small. Interestingly, when going back to "preferences" I suddenly see the "save" and "Cancel" button at the bottom of that window. :)
3. When zooming in to a genomic location, the annotation track disappears behind the Amino acid row (big letters). And now i realized that immediately above there is a tiny base pair (and weaker contrast) letters.
4. the genomic location track at the top also won't increase font size and stays small.
5. When selecting a track, The contract between background and text is weak. Maybe it is possible to have to background a little darker?

Tomorrow, I will try the other dark mode.
Thanks again. I am loving it!

Cheers
Tom

[jrobinso]

@chuddy-ibk Thanks for the test, issues like this are not unexpected. I will work through these, some may be unrelated to dark mode.

[jrobinso]

@chuddy-ibk WRT item 1, this is what I see on a Mac

I don't have access to a Linux machine. It would be helpful to know if you see this in the released IGV, and also in the snapshot with other themes (non-dark). Also a screenshot of what the buttons look like would be helpful.