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neurodata / ndstore

code for storing neurodata images and image annotations
http://neurodata.io
Apache License 2.0
38 stars 12 forks source link

ingest bigneuron data #259

Closed jovo closed 8 years ago

jovo commented 8 years ago

https://github.com/BigNeuron/Data/releases

@Aeusman @j6k4m8 anybody want to look at it?

kunallillaney commented 8 years ago

@Aeusman Let's look at this after you are done with finals.

jovo commented 8 years ago

@kunallillaney good call! want to put a milestone with a date on this? up to you guys when, maybe last monday of may?

kunallillaney commented 8 years ago

I don't want to commit to a milestone for @Aeusman. Since he might have other things in the pipeline. I assigned it to him for now so we don't drop the ball over summer.

Aeusman commented 8 years ago

http://openconnecto.me/ocp/ca/allen_gold_16_012/image/xy/0/0,1000/0,1000/46/window/0,100/

Ingested

jovo commented 8 years ago

cool!!! can you send a ndviz link? @alexbaden

On Mon, Jul 25, 2016 at 12:35 PM, Alex Eusman notifications@github.com wrote:

http://openconnecto.me/ocp/ca/allen_gold_16_012/image/xy/0/0,1000/0,1000/46/window/0,100/

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alexbaden commented 8 years ago

Traveling today. viz.neurodata / token / channel /

Will need to be windowed in the console first or you'll cache black tiles.

Alex

On Mon, Jul 25, 2016 at 13:21 joshua vogelstein notifications@github.com wrote:

cool!!! can you send a ndviz link? @alexbaden

On Mon, Jul 25, 2016 at 12:35 PM, Alex Eusman notifications@github.com wrote:

http://openconnecto.me/ocp/ca/allen_gold_16_012/image/xy/0/0,1000/0,1000/46/window/0,100/

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jovo commented 8 years ago

i tried using the token listed with channel "image". it looks all black.

i tried changing the max intensity using the scroll bars. but i didn't know the values it had, and it still looked black.

Aeusman commented 8 years ago

The first ~15 slices appear to be mostly black/contain no data (at least for this dataset)

alexbaden commented 8 years ago

Yup, it will be black until a window is set in ndstore and memcached is flushed. On Mon, Jul 25, 2016 at 13:26 joshua vogelstein notifications@github.com wrote:

i tried using the token listed with channel "image". it looks all black.

i tried changing the max intensity using the scroll bars. but i didn't know the values it had, and it still looked black.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/neurodata/ndstore/issues/259#issuecomment-235057500, or mute the thread https://github.com/notifications/unsubscribe-auth/AFkzUjZ9aghY-XKgcKC6JfS27GRnBhTkks5qZQ22gaJpZM4IBicj .

jovo commented 8 years ago

shouldn't the "max" slider do that dynamically?

alexbaden commented 8 years ago

Nope. The problem is the 16 bit data is rendered to 8 bits on the server. The window tells the server how to handle that resampling. The client can do some minimal tweaking of the 8bit data, but if your range is 0-1000 and you sample 0,2^16 into 0,2^8, all your data is lost as noise and the 8bit image ends up black.

We could look into rendering 16 bit data on the client to get around this problem, especially since datascope / MySQL isn't reliable enough to run big histogram jobs at the moment. Something to discuss Weds or next week.

Alex On Mon, Jul 25, 2016 at 13:36 joshua vogelstein notifications@github.com wrote:

shouldn't the "max" slider do that dynamically?

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jovo commented 8 years ago

ok. let's put an issue in ndviz to create a project for this with appropriate windowing?

Aeusman commented 8 years ago

I think my comment was misinterpreted, even when manually windowing the data by pulling pngs the first ~15 slices are blank. but at slice 46 we can see data so I would recommend testing based on that.