Data Import

How to get image data into the system

Adding the MouseLight Open Data

The MouseLight project at Janelia has made available the complete imagery and neuron tracing annotations for its published data sets on the AWS Open Data Registry.

You can easily make these available in your own HortaCloud instance by creating a Synchronized Folder which points to /s3data/janelia-mouselight-data.

Adding a single volume

A Horta Sample is an object representing a single 3D volume that can be visualized and traced with Horta.

If you already have the HortaKTX format data in your mounted S3 buckets, select FileNewHorta Sample, and then set “Sample Name” to <sampleDirectoryName> and “Path to Render Folder” as /s3data/<bucketName>/<sampleDirectoryName>.

Open the Data Explorer (WindowCoreData Explorer) and navigate to Home, then “3D RawTile Microscope Samples”, and your sample name. Right-click the sample and choose “Open in Horta”. This will open the Horta Panel and then from the Horta Panel you have options to create a workspace or to open the 2D or the 3D volume viewer.

Converting your data

If your data has not been converted into HortaKTX format, you can use the HortaCloud Data Importer to convert it. This tool supports many common image formats, and can be easily extended in Python to support your favorite format.

Last modified November 9, 2022: added synchronized folders docs (f9e5486)