tiff files in galaxy
Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access.
Hi, Robert As far as I know, all browsers besides Safari aren't set up to render tiff files by default. Are you using Safari to display the files in Galaxy? There are extensions for Firefox and Chrome that will allow you to display these files. Would that be an option? As a side note: creating, saving, and manipulating images and thumbnails would require Galaxy including a server side image processing library as a dependency. I'd like to do this at some point in the future as it would allow us other advantages too. Thanks, Carl On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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I was planning to use server code to tile the large images and then use one of a number of JavaScript libraries to render. Any browser should work without extensions . Jim did this with visigene in the genome browser years ago. - Robert
On Dec 3, 2013, at 9:16 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hi, Robert
As far as I know, all browsers besides Safari aren't set up to render tiff files by default. Are you using Safari to display the files in Galaxy?
There are extensions for Firefox and Chrome that will allow you to display these files. Would that be an option?
As a side note: creating, saving, and manipulating images and thumbnails would require Galaxy including a server side image processing library as a dependency. I'd like to do this at some point in the future as it would allow us other advantages too.
Thanks, Carl
On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote: Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
VisiGene only sends gif and jpeg over the wire. -- James Taylor, Associate Professor, Biology/CS, Emory University On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote:
I was planning to use server code to tile the large images and then use one of a number of JavaScript libraries to render. Any browser should work without extensions . Jim did this with visigene in the genome browser years ago. - Robert
On Dec 3, 2013, at 9:16 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hi, Robert
As far as I know, all browsers besides Safari aren't set up to render tiff files by default. Are you using Safari to display the files in Galaxy?
There are extensions for Firefox and Chrome that will allow you to display these files. Would that be an option?
As a side note: creating, saving, and manipulating images and thumbnails would require Galaxy including a server side image processing library as a dependency. I'd like to do this at some point in the future as it would allow us other advantages too.
Thanks, Carl
On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch <baertsch@soe.ucsc.edu> wrote:
Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
If you wanted to implement fancier tiling and display for tiff, the extension point for this would be in the datatype's display_data method. You can use this to do whatever you'd like, displaying an intermediate page with relevant code for tiling, etc. See datatypes/tabular.py's display_data method for an example of the chunking tabular display. On Tue, Dec 3, 2013 at 12:59 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
I was planning to use server code to tile the large images and then use one of a number of JavaScript libraries to render. Any browser should work without extensions . Jim did this with visigene in the genome browser years ago. - Robert
On Dec 3, 2013, at 9:16 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hi, Robert
As far as I know, all browsers besides Safari aren't set up to render tiff files by default. Are you using Safari to display the files in Galaxy?
There are extensions for Firefox and Chrome that will allow you to display these files. Would that be an option?
As a side note: creating, saving, and manipulating images and thumbnails would require Galaxy including a server side image processing library as a dependency. I'd like to do this at some point in the future as it would allow us other advantages too.
Thanks, Carl
On Thu, Nov 21, 2013 at 4:17 PM, Robert Baertsch <baertsch@soe.ucsc.edu>wrote:
Do you know a fast way to open large tiff files in galaxy ? The sniffer recognizes the type, but clicking on the eyeball on a large 82mb file just hangs. Downloading the file and opening in preview does work but it is clunky. Perhaps storing a low res version that would be display when clicking the eyeball would speed access. ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
participants (4)
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Carl Eberhard -
Dannon Baker -
James Taylor -
Robert Baertsch