Changelog

Source: NEWS.md

fishr (development version)

• read_fish_neurons() and fish_roi_meshes() now expect fish2 skeletons and ROI meshes in nm, matching the change on the fish2 neuprint server (September 2026). Previously the default units = "nm" output was 16x too large. Skeleton radii are now also correctly scaled for every units option. If neuprint advertises a skeletonSize for the dataset, read_fish_neurons() uses it to calibrate skeletons.

fishr 0.3.0

Several new features including a L/R-side classifier, soma-position helpers and a unified xyz coordinate converter, plus DVID body lookup at points.

What’s Changed

• Add fish_point_side() to predict the L/R/M side of points in fish2 space by applying mirror_fish() and measuring the signed y displacement across the midline; supports units = "nm" / "raw" / "emraw" / "microns", a configurable midline threshold and rval = "side" / "distance". By @jefferis in https://github.com/flyconnectome/fishr/pull/4
• Add fish_somapos() and fish_soma_side() for soma queries against fish2 metadata. fish_somapos() returns an Nx3 matrix of soma positions (preferring somaLocation, falling back row-wise to tosomaLocation) in the requested units; fish_soma_side() classifies the logical side of each body via auto / instance (_L/_R/_M/_U suffix) / position (fish_point_side() on the soma), with manual reserved for a future somaSide column. By @jefferis in https://github.com/flyconnectome/fishr/pull/4
• Add fish_coords() as a single public converter between fish2’s voxel scales: nm, raw (the (16, 16, 15) nm grid stored in neuprint’s somaLocation and accepted by the DVID segmentation/labels endpoint), emraw (the (8, 8, 30) nm acquisition grid used in Clio / Neuroglancer URLs) and microns. as_character = TRUE returns "x,y,z" strings via nat::xyzmatrix2str(). By @jefferis in https://github.com/flyconnectome/fishr/pull/7
• Add fish_xyz2bodyid() to look up the segmentation body id at each 3D point via malevnc::manc_xyz2bodyid(), returning character ids. Default units = "emraw" matches the typical interactive case of pasting coordinates from a fish2 neuroglancer URL; raw, nm and microns are also accepted. By @jefferis in https://github.com/flyconnectome/fishr/pull/7
• Fix fish_neuprint_meta(NULL) to return the same soma-related columns (somaLocation, nsoma, somaSide, …) as fish_neuprint_meta(ids) by passing the full possibleFields list to neuprintr::neuprint_get_meta() on the all-bodies code path. By @jefferis in https://github.com/flyconnectome/fishr/pull/4
• Refactor fish_point_side() and fish_somapos() to delegate unit conversion to fish_coords() (and both gain "emraw" as a units value). fish_somapos() now returns matrices with natverse-standard uppercase X/Y/Z column names. By @jefferis in https://github.com/flyconnectome/fishr/pull/7

fishr 0.2.0

First versioned release with a NEWS file.

What’s Changed

• Add fish_clio_annotations() to read live Clio body annotations for fish2 (wraps malevnc::manc_body_annotations()) by @jefferis in https://github.com/flyconnectome/fishr/pull/2
• Add mirror_fish() and the underlying fish2_mirror_reg thin plate spline registration for mirroring across the fish2 midline. Ported from Philipp Schlegel’s navis-fishbrains landmarks; data-raw/fish2_mirror_reg.R recreates the registration from the upstream CSV. Verified against navis.mirror_brain(template = "Fish2", mirror_axis = "y") to sub-nanometre precision. By @jefferis in https://github.com/flyconnectome/fishr/pull/3
• Stylise the dataset name as lowercase fish2 throughout docs and titles
• Doc polishing and pkgdown reference index cleanup