problems downloading from VFB

[Leslie Griffith]

Here is a brief description of what I did and what happens.

1. I aligned my cells/GAL4s with the brain and it all looks beautiful

2. I hit “download” and chose .OBJ (the other options are not openable with any software I have). I get multiple files downloaded: the brain template .OBJ and for each GAL4 or cell a seperate .OBJ

3. I click on the brain template, it opens in photoshop and get this message

4. I do what it says. Also tried NOT doing what it said but results are the same.

5. I can see the brain template. I can display brain as dots or lines with no surface, but this does not affect the display of other cells/GAL4s

6. When I open a GAL4 file I see this- i.e. nothing. Can’t find a way to make the cells appear. I can also “add” the GAL4 to the template window but it does not show anything either

7. I am running Photoshop 22.3.1 on a Mac with OS 10.15.7

thanks!!

Leslie

Leslie C. Griffith MD PhD
Nancy Lurie Marks Professor of Neuroscience

Director, Volen National Center for Complex Systems
Brandeis University MS008

415 South St.
Waltham, MA 02454-9110
781 736 3125
grif...@brandeis.edu

[Dr Gregory Jefferis]

Hi Leslie,

Let's see what Rob Court from VFB has to say but I've never tried to use Photoshop to display obj files. I normally do this using our command line tools based in R (natverse.org) but for a GUI you could try https://github.com/takashi310/VVD_Viewer developed at Janelia. This lets you display multiple meshes, turn them on and off, change colours etc.

All the best,

Greg.

On 18 Jan 2023, at 17:26, Leslie Griffith wrote:

> Here is a brief description of what I did and what happens.
>
> 1. I aligned my cells/GAL4s with the brain and it all looks beautiful
>
> 2. I hit “download” and chose .OBJ (the other options are not openable with any software I have). I get multiple files downloaded: the brain template .OBJ and for each GAL4 or cell a seperate .OBJ
>
> 3. I click on the brain template, it opens in photoshop and get this message
>
>
>

> 4. I do what it says. Also tried NOT doing what it said but results are the same.
>
> 5. I can see the brain template. I can display brain as dots or lines with no surface, but this does not affect the display of other cells/GAL4s
>
>

> 6. When I open a GAL4 file I see this- i.e. nothing. Can’t find a way to make the cells appear. I can also “add” the GAL4 to the template window but it does not show anything either
>
>
>

> 7. I am running Photoshop 22.3.1 on a Mac with OS 10.15.7
>
> thanks!!
>
> Leslie
>
> Leslie C. Griffith MD PhD
> Nancy Lurie Marks Professor of Neuroscience
> Director, Volen National Center for Complex Systems
> Brandeis University MS008
> 415 South St.
> Waltham, MA 02454-9110
> 781 736 3125
> grif...@brandeis.edu

--
Gregory Jefferis, PhD Tel: +44 1223 267048
Division of Neurobiology
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge, CB2 0QH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis
http://jefferislab.org
http://www.zoo.cam.ac.uk/research/groups/connectomics

[Leslie Griffith]

Sadly, I would not know a GUI if I stepped in one, and I don’t program. Was hoping for a dinosaur solution but I will see what happens when I click the link you sent! Fingers crossed!

Leslie C. Griffith MD PhD
Nancy Lurie Marks Professor of Neuroscience

Director, Volen National Center for Complex Systems
Brandeis University MS008

415 South St.
Waltham, MA 02454-9110
781 736 3125
grif...@brandeis.edu

[Leslie Griffith]

HI Rob:

I downloaded VVD, put it in my application folder, control-clicked it, and told my computer to live dangerously and open it, but it won’t stay open….keeps quitting by itself….

Leslie

Leslie C. Griffith MD PhD
Nancy Lurie Marks Professor of Neuroscience

Director, Volen National Center for Complex Systems
Brandeis University MS008

415 South St.
Waltham, MA 02454-9110
781 736 3125
grif...@brandeis.edu

[Greg Jefferis]

On 18 Jan 2023, at 17:59, Leslie Griffith <grif...@brandeis.edu> wrote:

I downloaded VVD, put it in my application folder, control-clicked it, and told my computer to live dangerously and open it, but it won’t stay open….keeps quitting by itself….

Ah, I have the impression that newer versions are not tested on older software/hardware – I am still running maocsx 10.15 (3 versions behind) and it doesn't run the latest versions of VVD viewer. 

You can try this version from April 2021:

https://github.com/takashi310/VVD_Viewer/releases/download/1.2.1/VVDViewer040921-macosx-vulkan-beta.dmg

There's a good chance this will work for you (it does for me).

Best,

Greg.

[Leslie Griffith]

OK I now see a neuron…I will continue to play with this. Thanks for getting me started!!

Leslie

Leslie C. Griffith MD PhD
Nancy Lurie Marks Professor of Neuroscience

Director, Volen National Center for Complex Systems
Brandeis University MS008

415 South St.
Waltham, MA 02454-9110
781 736 3125
grif...@brandeis.edu

[Rob Court]

Hey both,

I don't have a photoshop license to test this but I can guess the issue is that our files don't contain any materials data to define the surface. Most programs have a default surface material and don't mention anything, I assume this is what the 'Generate UVs' does.

As for the obj's for expression patterns or neurons, these are usually point clouds rather than meshes so just vector points with no surfaces which most programs will show if you just display points/vectors. 

VVD is a good option let me know if you have any more issues.

Thanks,

Rob

Virtual Fly Brain

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[Leslie Griffith]

THanks Rob- I am still having some issues but I need to play around some more. The beta version does run (a bit flaky tho- has crashed a few times).

But I will reach out to you when I get deeper into this with better questions! 

And leave poor Greg off the string!

thanks again to both of you- Leslie

Leslie C. Griffith MD PhD
Nancy Lurie Marks Professor of Neuroscience

Director, Volen National Center for Complex Systems
Brandeis University MS008

415 South St.
Waltham, MA 02454-9110
781 736 3125
grif...@brandeis.edu

On Jan 18, 2023, at 2:24 PM, Rob Court <rco...@ed.ac.uk> wrote:

Hey both,

I don't have a photoshop license to test this but I can guess the issue is that our files don't contain any materials data to define the surface. Most programs have a default surface material and don't mention anything, I assume this is what the 'Generate UVs' does.

As for the obj's for expression patterns or neurons, these are usually point clouds rather than meshes so just vector points with no surfaces which most programs will show if you just display points/vectors. 

VVD is a good option let me know if you have any more issues.

Thanks,

Rob

Virtual Fly Brain

On Wed, 18 Jan 2023 at 17:26, Leslie Griffith <grif...@brandeis.edu> wrote:

Here is a brief description of what I did and what happens.

1. I aligned my cells/GAL4s with the brain and it all looks beautiful

2. I hit “download” and chose .OBJ (the other options are not openable with any software I have). I get multiple files downloaded: the brain template .OBJ and for each GAL4 or cell a seperate .OBJ

3. I click on the brain template, it opens in photoshop and get this message

<Screen Shot 2023-01-18 at 10.59.51 AM.png>

4. I do what it says. Also tried NOT doing what it said but results are the same.

5. I can see the brain template. I can display brain as dots or lines with no surface, but this does not affect the display of other cells/GAL4s

<Screen Shot 2023-01-18 at 11.00.07 AM.png>

6. When I open a GAL4 file I see this- i.e. nothing. Can’t find a way to make the cells appear. I can also “add” the GAL4 to the template window but it does not show anything either

<Screen Shot 2023-01-18 at 10.59.31 AM.png>

7. I am running Photoshop 22.3.1 on a Mac with OS 10.15.7

thanks!!

Leslie

Leslie C. Griffith MD PhD
Nancy Lurie Marks Professor of Neuroscience

Director, Volen National Center for Complex Systems
Brandeis University MS008

415 South St.
Waltham, MA 02454-9110
781 736 3125
grif...@brandeis.edu