LGN-EM

Access the data:

• Install MoBIE-beta, following these instructions.
• Store the aws credentials so that the dataset can be loaded. For this, follow these instructions.
• Now, open the Fiji with MoBIE-beta and select Plugins->MoBIE->Open MoBIE Project ....
• Enter https://github.com/mobie/lgn-em-datasets in the prompt that opens.
• This should open a few menus and a viewer which shows the EM data.

Viewing the neuron segmentation:

• Select segmentation->neurons and click view in the MoBIE GUI (the menu with the whale logo)
• The current segmentation covers only a small part of the dataset, which is not part of the inital view. To find it, enter {"position":[326.64837813452584,119.43274034618811,31.013969544771427]} in location and click on move.

Saving interesting positions:

• You can save interesting positions by right click on a position in the viewer and then selecting BDV - Log Current View.
• This will print the position and view to the Log window; see below for an example output.
• The position can be recovered by pasting the line containing position (only changes position) or normalizedAffine (recvoers the full view) into the location menu.

{"position":[326.64837813452584,119.43274034618811,31.013969544771427],"timepoint":0}
{"affineTransform":[8.655308093335417,0.0,0.0,-2390.2423509426494,0.0,8.655308093335417,0.0,-744.2271641275895,0.0,0.0,8.655308093335417,-268.4354616073183],"timepoint":0}
{"normalizedAffine":[0.009903098504960432,0.0,0.0,-3.2348310651517727,0.0,0.009903098504960432,0.0,-1.182754192365663,0.0,0.0,0.009903098504960432,-0.3071343954317143],"timepoint":0}