janeliascicomp / neuronbridge

EM/LM neuron search

NeuronBridge

NeuronBridge is a web-based service for neuron matching and searching in Drosophila melanogaster. It indexes large data sets of LM and EM imagery to enable finding similar neurons across modalities and data sets. The software is described in this paper.

Source Code

This repository contains the web client. Other related repositories:

• neuronbridge-services - Backend implementation
• neuronbridge-aligners - Aligner implementation
• neuronbridge-precompute - Precompute scripts
• neuronbridge-python - Python API
• neuronbridge-vol-viewer - Web-based 3D Volume Viewer
• colormipsearch - Color Depth MIP Search Algorithms

Data Availability

The imagery and metadata are stored on AWS S3, and are available for browsing and reuse, subject to the license agreement:

• Color Depth MIPS
• Precomputed CDM match metadata
• Precomputed PPPM match metadata

Release Notes

View the Release Notes for a history of changes to the web client.

Development

Read the Developer's Guide for more information about developing and deploying this service.

License

All code related to NeuronBridge is made available under the 3-Clause BSD License.

All data served by the application is made available under the Creative Commons Attribution 4.0 International License.

Studies and publications that use this software should cite doi:10.1101/2022.07.20.500311.

neuronbridge's Issues

Replace line links with slide code links (Split-GAL4 and Gen1 MCFO)

Currently, NeuronBridge offers links in the search results to navigate to the line in question on the Split-GAL4 or Gen1 MCFO website. Suggest replacing this with a link to the slide code.
Normally, NeuronBridge supplies a link to the line:
https://splitgal4.janelia.org/cgi-bin/view_splitgal4_imagery.cgi?line=MB543B
This can be replaced with a link to a specific slide code:
https://splitgal4.janelia.org/cgi-bin/view_splitgal4_imagery.cgi?slidecode=20140407_33_G4

This is currently supported by the Split-GAL4 (splitgal4.janelia.org) and Gen1 MCFO (gen1mcfo.janelia.org) websites.

Password requirements are too complex

(I don't like to be "that guy" but at some point we must all make peace with who we are.)

The neuronbridge site requires a password that meets all of the following requirements:

• has minimum length
• contains lowercase letters
• contains uppercase letters
• contains numbers
• contains special characters

According to NIST password guidelines, it is against best practice to require any of those except for the first (minimum length).

To be fair, I could make this same criticism of many of the services I use on the internet, but for most of them I'm not sure where to register the complaint. You all, on the other hand, have the misfortune of being my colleagues, and I have access to your issue tracker.