Clarify the availability of the dataset

[jcohenadad]

I received the following email:

My name is XXX, and I am a PhD student in Computer science at XXX.
I am studying with XXX on the topic of biomedical image analysis.
Thanks to your helpful paper of "AxonDeepSeg: automatic axon and myelin segmentation from microscopy data using convolutional neural networks".
I would like to learn more about this topic.
If possible, would you please consider allowing me to work on the TEM dataset to train this model and other architectures.
https://github.com/axondeepseg/default-TEM-model
I will not redistribute the dataset without your consent.
If our project leads to publication, we will cite your paper.

Question: is the dataset publicly available? If not, can we make it available?

[mariehbourget]

The current BIDS version of the TEM dataset used to train the new ivadomed model is available on our git-annex server: data_axondeepseg_tem.

As we discussed in last week meeting, we did not open a repo with it because of its size ( ~ 2Gb).

The previous version of the dataset (non-BIDS) is still accessible on OSF here: https://osf.io/uewd9/
I would advise against using this version because:

• not BIDS compliant (not compatible with ivadomed)
• some correction were done with the BIDSification, see data_axondeepseg_tem: fuzzy masks neuropoly/data-management#135 (comment)

[jcohenadad]

Great! thank you @mariehbourget.

At some point, when our public-facing data sharing interface is ready, we will be able to offer the latest version of this dataset for download. Tagging @kousu @mguaypaq @taowa