Releases | Open Source Science

fafbseg - Version 3.1.3

This minor release contains two changes: - flywire.decode_url now also works with !middleauth+... URLs (thanks to @DanaSherman) - fixed an issue with flywire.get_mesh_neuron when with_synapses=True

- Python
Published by schlegelp 12 months ago

fafbseg - Version 3.1.2

Two minor fixes/changes: 1. Teach annotation function to properly shut up when verbose=False (fixes #21) 2. get_neuropil_volumes now returns a navis.Volume with its .units set. This required bumping the minimum version of navis to 1.8.0.

- Python
Published by schlegelp about 1 year ago

fafbseg - Version 3.1.1

This version includes a number of under-the-hood fixes: - revive the good old GSPointloader for datasets where there is no supervoxel look-up service - fix error in getcaveclient when using an unmaterialized non-FlyWire dataset - fix some issues related to numpy 2.0

- Python
Published by schlegelp about 1 year ago

fafbseg - Version 3.1.0

Improvements: - flywire.NeuronCriteria now works like an iterator - synced flywire.get_neuropil_volumes with precomputed://gs://flywire_neuropil_meshes/neuropils/neuropil_mesh_v141_v6 neuroglancer source

Fixes: - fixes a number of issues arising from numpy 2.0 - various other fixes

- Python
Published by schlegelp over 1 year ago

fafbseg - Version 3.0.10

This is a bug fix release for flywire.annotations.clear_cached_annotations().

- Python
Published by schlegelp almost 2 years ago

fafbseg - Version 3.0.9

Improved

flywire.fetch_adjacency now optionally returns per-neuropil connectivity (see docstrings for details)
flywire.search_annotation and flywire.get_hierarchical_annotations will now report the version used on first call

Fixed

fixed flywire.set_default_annotation_version
corrected a few docstrings

- Python
Published by schlegelp almost 2 years ago

fafbseg - Version 3.0.8

This release fixes a bug with caching the hierarchical annotations in Windows.

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.7

small fix for connectivity queries when filtered=True in the public dataset
queries against Github (for hierarchical annotations) will now use personal access token defined in GITHUB_PAT if present; this avoids issues with rate limits

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.6

Two small improvements: - (hierarchical) annotations can now be loaded from a specific (or just the latest) commit - re-enabled synapse queries against the raw (filtered=False) synapse table for the public dataset

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.5

This release fixes issues in flywire.get_adjacencies and flywire.get_connectivity when the query was against the live dataset.

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.4

This version fixes an accidentally introduced bottleneck in is_valid_root which caused a bunch of other functions to become sluggish.

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.3

Various bugfixes and improvements: 1. is_proofread (which is also used for connectivity queries) should now work with the public release data (see docstring for details) 2. get_cave_table will now optionally add user details (unclear if this works on public data) 3. various fixes for get_somas, find_mat_version, is_valid_root and is_latest_root

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.2

Another small bug fix that caused search_annotations to fail when local cache was empty.

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.1

This is a bug fix release:

Fixes an issue in search_community_annotations where adding user information for non-existent user "0" would fail
Prevents trying to query the live version if working with the public release datastack

- Python
Published by schlegelp about 2 years ago

fafbseg - Version 3.0.0

This is a major update with a few breaking changing!

Highlights:

The default dataset is now the "public" dataset.
It is now easy to work with annotations (classes, types, etc) instead of having to shuttle root IDs in and out of fafbseg functions; see the updated tutorial on annotations.
Annotation queries will download (and cache) data from https://github.com/flyconnectome/flywire_annotations which is currently principally based on Schlegel et al. (2023). We are planning to keep updating these annotations in the future.

We also renamed a bunch of functions to make things more consistent, please see the Changelog for details.

- Python
Published by schlegelp over 2 years ago

fafbseg - Version 2.0.3

One fix, one improvement: - flywire.fetch_connectivity now allows neuropils=True to return edges broken down by neuropils - fix flywire.predict_neuropils with single_pred=True

- Python
Published by schlegelp over 2 years ago

fafbseg - Version 2.0.2

Fixes a bug in connectivity queries when filtered=False and mat='live' that caused empty results (bug in CAVE).
flywire.update_ids:
- now deals better with StringArrays
- faster when timestamp is provide
flywire.get_skeletons now correctly loads radii information (requires navis update too)

- Python
Published by schlegelp over 2 years ago

fafbseg - Version 2.0.1

Minor bug fix.

- Python
Published by schlegelp over 2 years ago

fafbseg - Version 2.0.0

This release implements functionality to query & work with the public (v630) release of FlyWire.

This is a major release with various breaking changes. Please see the changelog for details.

- Python
Published by schlegelp over 2 years ago

fafbseg - Version 1.15.1

Tons of changes and improvements. Here are some of the highlights:

The FlyWire synapse/connectivity queries can now be run against the filtered table which is what you see in Codex. See the filtered parameters for these functions.
Improvements to the skeletonization.
flywire.get_mesh_neuron can now be run against the flat 630 segmentation which is much faster.

Tons of other improvements/fixes - please see the commit history for the full list.

- Python
Published by schlegelp almost 3 years ago

fafbseg - Version 1.14.0

The highlights for this release:

New function: flywire.meshes.mesh_neuron
Supervoxel/root look-ups not accept mat_{version} as timestamp parameter
Synapse/connectivity queries will now by default try to pick a materialization version matching the query IDs
New function: flywire.is_materialized_root
Added a render pipeline using Blender (tutorial pending)

Tons of other improvements/fixes - please see the commit history for the full list.

- Python
Published by schlegelp over 3 years ago

fafbseg - Version 1.13.0

New functions since 1.11.0 (accidentally skipped a version): - flywire.find_anchor_loc

Improvements: - flywire.get_neuropil_volumes can now also return a list of available neuropils - flywire.l2_skeleton now has an option that retains L2 IDs as node IDs - flywire.encode_url now lets you add multiple separate annotation layers - flywire.locs_to_segments and flywire.locs_to_supervoxels now also work with CloudVolume as backend (backup to spine) - flywire.update_ids is more robust and faster - flywire.skeletonize_neuron now lets you use threads for faster download - made a bunch of functions more robust to timeouts - loads of bugfixes

- Python
Published by schlegelp almost 4 years ago

fafbseg - Version 1.11.4

This is mostly a hot fix release but also contains two improvements: - flywire.update_ids now allows looking for a timestamp (slow!) - new function flywire.find_common_time lets you find a timestamp at which all given root IDs co-existed

- Python
Published by schlegelp almost 4 years ago

fafbseg - Version 1.11.3

Another hot fix for the Windows int issue

- Python
Published by schlegelp almost 4 years ago

fafbseg - Version 1.11.2

This release changes a few instances using Python's built-in int data type to np.int64. This should solve issues for Windows users where the default int type is only 32bit.

- Python
Published by schlegelp almost 4 years ago

fafbseg - Version 1.11.1

This minor release adds a single straggler: - new function, flywire.get_lr_position determines left/right side for given xyz coordinates

- Python
Published by schlegelp about 4 years ago

fafbseg - Version 1.11.0

This release contains among other things: 1. Various improvements for FlyWire annotation-related functions 2. New function: flywire.neuroglancer.neuron_to_url takes a skeleton and creates a link with overlapping FlyWire segments 3. flywire.update_ids now uses L2 IDs (instead of supervoxels) to determine which downstream root ID is the most likely successor. This is noticeable faster. 4. flywire.get_annotation_tables has been deprecated in favor of flywire.list_annotation_tables

- Python
Published by schlegelp about 4 years ago

fafbseg - Version 1.10.0

Small improvements and fixes: - l2_skeletons now uses threads and add radius (if available) - l2_dotprops now has an option to sub-sample the points - to fix issues with Windows where int defaults to 32bit, we now explicitly use np.int64 when dealing with root IDs - new function: flywire.get_neuropil_volumes will load neuropil meshes - flywire.encode_url now includes a (hidden) layer with brain mesh - various bug fixes

- Python
Published by schlegelp about 4 years ago

fafbseg - Version 1.9.0

new functions: flywire.get_lineage_graph, flywire.get_voxels, flywire.is_proofread (see docs for details)
added more/better retrying for L2 functions (e.g. flywire.l2_dotprops)
fixed a couple issues with FlyWire root IDs and int on Windows
various bug fixes

- Python
Published by schlegelp about 4 years ago

fafbseg - Version 1.8.0

Critically this version updates to the URLs for the servers hosting the FAFB14 <-> FlyWire deformation fields and FlyWire supervoxel lookups (required e.g. for flywire.locs_to_segments/supervoxels.

Additional changes/improvements: - flywire.update_ids now accepts optional supervoxels to speed-up updating root IDs - added checks to catch invalid root/supervoxel IDs throughout flywire functions