bunch a li'l things

[jovo]

• [x] it seems the navigation bar on the right doesn't indent the way i expected it to?
• [x] rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• [ ] Volume reconstruct: let's either remove it or add code to repo
• [ ] manno links to github repo, not github page?
• [ ] link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• [ ] same with CATMAID?
• [x] parity doesn't work, remove until it does? or at least say that it is not live?
• [x] macho link doesn't work
• [x] open-connectome thru ndio links are broken
• [x] AWS link doesn't work, and i think the name changes whenever @gkiar updates it, so we should write something like "AMI id:"neurodata....")
• [x] m2g link doesn't work
• [ ] what about RAMON, LONI, and "Further Reading", where do they go now?

[wrgr]

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein notifications@github.com wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

[wrgr]

Sorry - what's this?

• it seems the navigation bar on the right doesn't indent the way i expected it to?

(I don't see a nav bar at all, except the menu on the left?

On Wed, Sep 30, 2015 at 2:11 PM William R. Gray Roncal willgray@gmail.com wrote:

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein < notifications@github.com> wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

[jovo]

right, menu on the left. it is flat, but others have indentation structure?

On Wed, Sep 30, 2015 at 2:12 PM, William Gray notifications@github.com wrote:

Sorry - what's this?

• it seems the navigation bar on the right doesn't indent the way i expected it to?

(I don't see a nav bar at all, except the menu on the left?

On Wed, Sep 30, 2015 at 2:11 PM William R. Gray Roncal <willgray@gmail.com

wrote:

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein < notifications@github.com> wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1#issuecomment-144495433 .

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

[jovo]

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

the 3rd party tools we claim to support:

• CATMAID
• Vaa3D
• VAST
• BigDataViewer

we should be explicit which version we support, and before we push, ideally, the tests that we run include tests for them and CAJAL & ndio.

i'm not sure how much work this is or who would do it, it seems that our current system works ok, but could run much better.

hopefully, no more pushes before SfN, except for auto-ingest? perhaps we can push that asap, so we can work out any bugs it uncovers (one way or another)?

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein < notifications@github.com> wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1#issuecomment-144495128 .

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

[wrgr]

Ok - did the easy stuff. md requires http:// in front of all links - different than RST

The menu expands differently because this is md, not rst. If you hate the menu structure, I can rewrite in RST.

I think we need a list of things that must pass before the backend is updated. If you want to include the 3rd party tools, I think that's great. It's part of what the backend team should do prior to rolling things, imho, along with cajal.

On Wed, Sep 30, 2015 at 2:16 PM joshua vogelstein notifications@github.com wrote:

right, menu on the left. it is flat, but others have indentation structure?

On Wed, Sep 30, 2015 at 2:12 PM, William Gray notifications@github.com wrote:

Sorry - what's this?

• it seems the navigation bar on the right doesn't indent the way i expected it to?

(I don't see a nav bar at all, except the menu on the left?

On Wed, Sep 30, 2015 at 2:11 PM William R. Gray Roncal < willgray@gmail.com

wrote:

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein < notifications@github.com> wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

— Reply to this email directly or view it on GitHub < https://github.com/openconnectome/nddocs/issues/1#issuecomment-144495433> .

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar < https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1#issuecomment-144496690 .

[jovo]

ok, we should discuss at next ocp meeting that i attend (which won't be next week).

On Wed, Sep 30, 2015 at 2:22 PM, William Gray notifications@github.com wrote:

Ok - did the easy stuff. md requires http:// in front of all links - different than RST

The menu expands differently because this is md, not rst. If you hate the menu structure, I can rewrite in RST.

I think we need a list of things that must pass before the backend is updated. If you want to include the 3rd party tools, I think that's great. It's part of what the backend team should do prior to rolling things, imho, along with cajal.

On Wed, Sep 30, 2015 at 2:16 PM joshua vogelstein < notifications@github.com> wrote:

right, menu on the left. it is flat, but others have indentation structure?

On Wed, Sep 30, 2015 at 2:12 PM, William Gray notifications@github.com wrote:

Sorry - what's this?

• it seems the navigation bar on the right doesn't indent the way i expected it to?

(I don't see a nav bar at all, except the menu on the left?

On Wed, Sep 30, 2015 at 2:11 PM William R. Gray Roncal < willgray@gmail.com

wrote:

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein < notifications@github.com> wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

— Reply to this email directly or view it on GitHub < https://github.com/openconnectome/nddocs/issues/1#issuecomment-144495433

.

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar <

https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

— Reply to this email directly or view it on GitHub < https://github.com/openconnectome/nddocs/issues/1#issuecomment-144496690> .

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1#issuecomment-144498337 .

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

[jovo]

thanks

On Wed, Sep 30, 2015 at 2:47 PM, joshua vogelstein jovo@jhu.edu wrote:

ok, we should discuss at next ocp meeting that i attend (which won't be next week).

On Wed, Sep 30, 2015 at 2:22 PM, William Gray notifications@github.com wrote:

Ok - did the easy stuff. md requires http:// in front of all links - different than RST

The menu expands differently because this is md, not rst. If you hate the menu structure, I can rewrite in RST.

I think we need a list of things that must pass before the backend is updated. If you want to include the 3rd party tools, I think that's great. It's part of what the backend team should do prior to rolling things, imho, along with cajal.

On Wed, Sep 30, 2015 at 2:16 PM joshua vogelstein < notifications@github.com> wrote:

right, menu on the left. it is flat, but others have indentation structure?

On Wed, Sep 30, 2015 at 2:12 PM, William Gray <notifications@github.com

wrote:

Sorry - what's this?

• it seems the navigation bar on the right doesn't indent the way i expected it to?

(I don't see a nav bar at all, except the menu on the left?

On Wed, Sep 30, 2015 at 2:11 PM William R. Gray Roncal < willgray@gmail.com

wrote:

ok - I'll work on this. Another side effect of the backend updates is that someone really needs to go through the third party tools - vaa3d is broken, as is bigdata viewer and possibly other things.

I think we (meaning me) should send a note to each of the 3rd party partners and invite them to write a quick markdown page. If they don't want to, we'll git issue internally and do asap? I know VAST has a protocol, for example.

On Wed, Sep 30, 2015 at 2:03 PM joshua vogelstein < notifications@github.com> wrote:

• it seems the navigation bar on the right doesn't indent the way i expected it to?
• rename misha's code to "2D Color Correction" (because the other name is not clear what it does to our user community)
• Volume reconstruct: let's either remove it or add code to repo
• manno links to github repo, not github page?
• link to VAST: does their documentation explain how to use OCP with them? if not, we should document; if we don't, we should just make a "blank" documentation page that says VAST supports it, but there is no documentation?
• same with CATMAID?
• parity doesn't work, remove until it does? or at least say that it is not live?
• macho link doesn't work
• open-connectome thru ndio links are broken
• AWS link doesn't work, and i think the name changes whenever @gkiar https://github.com/gkiar updates it, so we should write something like "AMI id:"neurodata....")
• m2g link doesn't work
• what about RAMON, LONI, and "Further Reading", where do they go now?

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1.

— Reply to this email directly or view it on GitHub <

https://github.com/openconnectome/nddocs/issues/1#issuecomment-144495433>

.

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar <

https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

— Reply to this email directly or view it on GitHub < https://github.com/openconnectome/nddocs/issues/1#issuecomment-144496690> .

— Reply to this email directly or view it on GitHub https://github.com/openconnectome/nddocs/issues/1#issuecomment-144498337 .

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York

the glass is all full: half water, half air. openconnecto.me, medhacks http://medhacks.org/, calendar https://www.google.com/calendar/embed?src=afr9t36kknt629jh4omun20n90%40group.calendar.google.com&ctz=America/New_York