Catmaid login inquiry

[jiaxin Gong]

Dear Sir/Madam,

My name is Jiaxin Gong and I am a principle investigator from southern medical university in China. I am recently learning Catmaid for circuit mapping. I am writing to inquire about how to login at catmaid.virtualflybrain.org. I am not sure whether it’s allowed to create user's own project or not. Thanks so much for the help!

Sincerely,

Jiaxin Gong

[Rob Court]

Dear Jiaxin,

Thank you for your email.

Unfortunately, we only host finalised published data on each of the catmaid instances we host on behalf of the groups who created the data. CATMAID is available to run on your own infrastructure to set up your project for free: https://github.com/catmaid/CATMAID 

If you wanted to add tracings to existing stacks/projects then you'd need to contact the individual project groups to get involved via them.

We hope to host your data when you are ready to release it to the public.

Best of luck,

Dr Robert Court

VirtualFlyBrain.org

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[jiaxin Gong]

Dear Rob,

Sorry for bothering you again! It's been almost a year since the last contact..... I tried setting up CATMAID tool on and off for the past several months, and finally it seems running now (at least I think). Next I want to load the drosophila L1 EM dataset and do some tracing. Unfortunately, I couldn't find a clear instruction as to how and where to access the image stacks. I tried the VFB L1 catmaid instance within the Importer tool in CATMAID, but got errors probably linked to connection issues? So I am not sure whether VFB allows public access to the original L1EM dataset? Any suggestions would be appreciated!

Sincerely,

Jiaxin

On Tue, Jul 23, 2024 at 5:00 PM Rob Court <rco...@ed.ac.uk> wrote:

Dear Jiaxin,

Thank you for your email.

Unfortunately, we only host finalised published data on each of the catmaid instances we host on behalf of the groups who created the data. CATMAID is available to run on your own infrastructure to set up your project for free: https://github.com/catmaid/CATMAID 

If you wanted to add tracings to existing stacks/projects then you'd need to contact the individual project groups to get involved via them.

We hope to host your data when you are ready to release it to the public.

Best of luck,

Dr Robert Court

VirtualFlyBrain.org

On Sat, 20 Jul 2024 at 09:17, jiaxin Gong <bingl...@gmail.com> wrote:

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[Alex McLachlan]

Dear Jiaxin,

If you are looking to trace neurons in the L1 EM dataset the VFB instance only has those neurons which have been released as part of a publication. If you wanted to contribute to the overall tracing effort you could contact Albert Cardona to get access to the live CATMAID server if you have not done so already? I was under the impression that this dataset was nearing completion however.

To get the image stacks for your own CATMAID instance you may want to contact Tom Kazimiers.

Best,

Alex