PyReconstruct is a downloadable annotation tool useful for tracing and identifying ultrastructural cell features. It is actively maintained by the Kristen Harris lab at the University of Texas at Austin. To annotate BossDB-hosted image volumes using PyReconstruct, download a subvolume using this webpage, then import it into PyReconstruct using the guide below.
Questions? Reach us at info@bossdb.org.
First, construct the BossDB path(s) where your data of interest is stored.
To construct the paths, browse https://metadata.bossdb.org
to find the data of interest. Copy into the box the collection,
experiment, and channel formatted as bossdb://<collection>/<experiment>/<channel>.
An example of a BossDB path is bossdb://nguyen_thomas2022/cb2/em.
Its metadata page is found here
and its collection, experiment, and channel are the title of the webpage.
First, install and start PyReconstruct. The instructions are found in the official README.
Next, unzip the file you downloaded. Import it into PyReconstruct using
the File > New > From neuroglancer zarr... menu option. Follow the menus
through until the import has completed.
After import, the view may still appear black. If so, use the View >
Set view to image menu option.
