How to mount the data repository
The data repository can be found here or mounted as descibed below.
There is no password or username necessary for read-only access.
Simply press “Map network drive” from the Windows Explorer and enter the link provided above.
sudo mount -t davfs https://synem.rzg.mpg.de/webdav SOME_MOUNTPOINT (make sure you have the related packages)
Brief explanantion of content
The content is located in two main folders:
- Classifier, the trained SynEM classifiers including the interface annotations in the training and validation regions as well as the precalculated interface features
- TestSet, the raw and segmentation data of the test set and ground truth annotations for all synapses and excitatory spine synapses
- The data used to train and evaluate SynEM on a dataset from ATUM-SEM (Kasthuri et al., 2015)
Detailed explanation of content
- The boosted decision-stump classifier trained on all features (SynEMPaperClassifier.mat) and only on the features with positive feature importance (SynEMPaperClassifierPred.mat)
- The 40 training/validation volumes containing interfaces and interface labels (/Classifier/SynapseDetectionTrainingDataRevised)
- The features calculated from the training and validation cubes (/Classifier/train, /Classifier/val)
Test set (/TestSet)
- The SynEM test set ground truth containing all synapses (TestSet_allSyn_gt.mat) and excitatory spine synapses only (TestSet_excSyn_gt.mat)
- The SynEM test set raw data and segmentation (TestSet_raw_seg.mat) (see also +SynEM/+Examples/synEMWorkflow.m in the SynEM repository)
Ground truth data and the trained classifier used for the evaluation of SynEM on the ATUM-SEM dataset from Kasthuri et al. (2015). See also the scripts downloadDatasetScript.m, labelGeneration.m and trainSynEM.m in the KasthuriData package in the SynEM repository.
- kat11_seg_modified.zip: The modified segmentation created for the evaluation of SynEM as described in the “Evaluation on the dataset from Kasthuri et al. (2015)” method section in the SynEM paper.
- KasthuriDirClassifier.mat: The trained SynEM classifier.
- SynapseDirectionLabels_v3.mat and synapseDirectionGT_v3.mat: The interface ground truth data.
- local/: Tiling of the dataset into non-overlapping cubes containing the supervoxel graph data for each local cube and the SynEM interface features.
- global*.mat files: The supervoxel graph data collected from the single tiles in local/*.
- allParameter.mat: The paths to the folders and files in local/* (see p.local).