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adwanner / PyKNOSSOS

PyKNOSSOS is a software tool for the visualization and annotation of 3D image data and was developed for high-throughput image annotation of 3D electron microscopy stacks of brain tissue. https://www.ariadne.ai
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Getting skeleton and synapse data from Pyknossoss #1

Closed dadanhan closed 2 years ago

dadanhan commented 2 years ago

Hi, I was just wondering how to get skeleton and synapse data from the .nmx files?

adwanner commented 2 years ago

Hi, for the record: NMX-file is a zip-archive container in which annotations and skeletons are saved in individual NML-files, the native KNOSSOS file format, which is XML-based. Each skeleton consists of 3D nodes (vertices) connected by edges. The NML format was originally described in https://www.nature.com/articles/nn.2868?page=5

dadanhan commented 2 years ago

Hi, thanks for the answer. I managed to read in the skeletons and now I am wondering if synapse information was also included in 'Dataset 2: Skeleton reconstructions of neurons in the OB' from https://www.nature.com/articles/sdata2016100 How would I be able to get skeleton reconstructions and synapse locations along the skeletons from PyKNOSSOS/dataset 2?

adwanner commented 2 years ago

the synapses have been annotated in a follow-up study (https://www.nature.com/articles/s41593-019-0576-z). I can add them to the zenodo repository if you are interested. Note, however, some of the synapses have been annotated redundantly. A detailed description of the synapse annotation procedure can be found in the paper.

dadanhan commented 2 years ago

Hi that would be great to have some synapse data! I've also sent you an email from my academic address.

adwanner commented 2 years ago

where did you send it to? I have not received anything yet...

dadanhan @.***> schrieb am Do., 2. Dez. 2021, 18:49:

Hi that would be great to have some synapse data! I've also sent you an email from my academic address.

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dadanhan commented 2 years ago

Hi, I sent it to the @fmi.ch email that was the corresponding email in the Nature articles. Is it ok? Please let me know a more recent one if that is not valid.

dadanhan commented 2 years ago

Hi Adrian, sorry I was looking at the older Nature publication. I realized that you are now in Princeton and have sent you another email. Please let me know if this is correct.