Downloading stacks

[Gabi Avihsai]

Dear VFB team,

Is it possible to download raw/aligned stacks of the Flycircuit dataset? I would like to find Neuronbridge matches for some of this dataset's neurons.

Best,

Gabi

 

Gabi Avishai

Ph.D student

The lab of Dr. Moshe Parnas

Department of Physiology and Pharmacology

Sackler Faculty of Medicine

Tel Aviv University

[Robbie Court]

Dear Gabi,

Thank you for your interest in the Virtual Fly Brain (VFB) resources.

Yes, it is possible to download raw/aligned stacks of the Flycircuit dataset. You can use our Bulk Download tool for this purpose. Here is a brief guide on how to use it:

1. Navigate to the VirtualFlyBrain.org website and open all the images you are interested in downloading.
2. Locate the bulk download icon (fa-download) on the website. Click on this icon to open the bulk download tool.
3. In the bulk download tool, select the type of data you want to download. The options are OBJ, SWC, NRRD, and References.
4. After making your selections, click the 'Download' button to start the download. The data will be downloaded in a zip file named "VFB Files.zip".
5. Once the download is complete, locate the zip file in your downloads folder and unzip it to access the data.

For more detailed instructions, please refer to our Bulk Download Guide.

To find Neuronbridge matches for some of the dataset's neurons, you can use our Similarity Score Queries feature. Here's a brief guide:

1. Navigate to the Term Info section on VirtualFlyBrain.org and select a neuron or expression pattern of interest.
2. Under the 'Query For' section, locate the 'Find similar...' expandable menu. This menu will only appear if an above-threshold score is available for the selected neuron or expression pattern.
3. Inside the 'Find similar...' menu, you will find queries to find morphologically similar neurons or expression patterns. Select a query to run it.

For more detailed instructions, please refer to our Similarity Score Queries Guide.

Additionally, you may also find our API tool, VFBconnect, useful for programmatically accessing and downloading data from VFB. You can find more information about VFBconnect here.

Please let us know if you have any other questions or need further assistance.

Best regards,

Rob Court
VFB Team

[Gabi A]

Hi Rob,

Thank you very much for your helpful response. 

I downloaded the data as you suggested, and it works well. I guess that earlier I downloaded the separate files, and the number of slices in the signal channels (the neuron and the template) was not compatible, thus prevented me from merging them.

Any how, it's fine now.

Thanks again,

Gabi