Data Access

To enable pipleline development and benchmarking, we have identified several test datasets. We host an publicly accessible Electron Microscopy Dataset (from Kasthuri et al., 2015 https://www.sciencedirect.com/science/article/pii/S0092867415008247) and an X-ray microtomography dataset (from Dyer et al., 2017 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5659258/). We also provide a link to data from the Allen Institute Reference Atlas for 2-D cell detection examples.

Data Access for EM and X-ray dataset:

Data can be accessed, visualized, and downloaded from our bossDB database here: https://api.bossdb.io. In the configuration yaml files for our example workflows, use the access token below.

General:

• boss console login: https://api.bossdb.io/v1/mgmt/
• neuroglancer (for visualization): https://neuroglancer.bossdb.io Details:
• Username: public-access
• Password: public
• Public_Access_Token: public If the public access token has changed, please log into api.bossdb.io using the above credentials and go to public-acces->api_token to find the current token.

Electron Microscopy Dataset:

• Coll: Kasthuri
• Exp: em
• Chans: images, I2G_Membranes_i_Pub, I2G_Neuron_Seg_Pub, I2G_Synapses_i_Pub
• Coord: KasthuriFrame
• link: https://api.bossdb.io/v1/mgmt/resources/Kasthuri/em

X-ray Microtomography Dataset:

• Coll: XBrainGTech5
• Exp: Proj4
• Chans: full_vol, membranes_Pub, vessels_Pub, cells_Pub
• Coord: XBrain_ingest_coord2
• link: https://api.bossdb.io/v1/mgmt/resources/XBrainGTech5/Proj4

Downloading data to a local file:

You can use our boss access tool to download data locally in addition to using it in containerized workflows. https://github.com/aplbrain/saber/tree/master/saber/boss_access

To build the container: docker build -t boss-access .

To run the container: docker run -it -v $(pwd)/data:/data/ boss-access /bin/bash

To download example Electron Microscopy data (use public access token above):

boss_access.py pull -t <Public_Access_Token> --host api.bossdb.io --coll Kasthuri --exp em --chan images --coord KasthuriFrame --dtype uint8 --itype image --res 1 --xmin 5990 --xmax 7824 --ymin 6059 --ymax 7892 --zmin 610 --zmax 620 --padding 0 -o /data/em_images.npy

To download example X-ray microtomography data (use public access token above):

boss_access.py pull -t <Public_Access_Token> --host api.bossdb.io --coll XBrainGTech5 --exp Proj4 --chan rodrilm2 --coord XBrain_ingest_coord2 --dtype uint8 --itype image --res 0 --xmin 1100 --xmax 1400 --ymin 1000 --ymax 1300 --zmin 300 --zmax 600 --padding 0 -o /data/xray_data.npy

Example data for 2-D Cell Detection from Allen Institute Reference Atlas data:

We also provide an example workflow for detection of cell bodies from 2-D Brain Atlas data collected at the Allen Brain Institute (Lein, E.S. et al. (2007) Genome-wide atlas of gene expression in the adult mouse brain, Nature 445: 168-176. doi: 10.1038/nature05453.)

The data are hosted by the Dyer Lab (https://github.com/nerdslab/celldetect) and can be downloaded here: https://www.dropbox.com/s/f21jpjad487f1nv/celldetect-demo-data.zip?dl=0

Example Visualization:

Here is an example visualization of EM data:

• x-range: [5000, 6000]
• y-range: [8620, 9620]
• z-range: [400, 405]
• resolution: 0
• neuroglancer link: https://neuroglancer.bossdb.org/#!{'layers':{'images':{'type':'image'_'source':'boss://https://api.bossdb.org/Kasthuri/em/images'}_'I2G_Membranes_i_Pub':{'type':'image'_'source':'boss://https://api.bossdb.org/Kasthuri/em/I2G_Membranes_i_Pub'_'visible':false}_'I2G_Synapses_i_Pub':{'type':'image'_'source':'boss://https://api.bossdb.org/Kasthuri/em/I2G_Synapses_i_Pub'_'visible':false}_'I2G_Neuron_Seg_Pub':{'type':'segmentation'_'source':'boss://https://api.bossdb.org/Kasthuri/em/I2G_Neuron_Seg_Pub'}}_'navigation':{'pose':{'position':{'voxelSize':[3_3_30]_'voxelCoordinates':[5448.3203125_9158.8349609375_403]}}_'zoomFactor':6.060436461202043}_'layout':'xy'}