NEWS.md

In jefferis/elmr: Support for working with light and electron microscopy fly brain data

elmr 0.6

• move general purpose functions to nat. See #50.
• prune_twigs
• distal_to
• stitch_neuron
• stitch_neurons
• tpsreg
• plot3d.ngraph

elmr 0.5.7

• switch repo to natverse github organisation

elmr 0.5.6

• new prune_twigs() function that removes twigs less than a threshold length. Useful thing to do as part of preparing dotprops() objects for nblast().
• Fix strange arrows in plot3d.ngraph() (#45)
• Allow open_fafb() to specify a different CATMAID server (including via a catmaid_connection() object) (#44)
• Teach nblast_fafb() to prune twigs by default
• fix hitherto silent bugs revealed by R 3.6

elmr 0.5.5

• teach open_fafb() to make many URLs at once e.g. for results of tagged_details (#41)

elmr 0.5.4

• add plot3d.ngraph() (shows directed graph in 3d)
• fix simplify_neuron() when spine has 1 branch only (#40)
• vignette tweaks

elmr 0.5.3

• teach simplify_neuron() to handle the inverse as well (#38)
• change IVLP -> WED in FAFBNP surfaces as well as FAFB14NP (#35)
• teach fetchn_fafb to work even if FAFB is given as the reference brain (#39)

elmr 0.5.2

• teach simplify_neuron() to handle arbitrary number of branch points (#37)
• minor doc fixes

elmr 0.5.1

• teach distal_to() to handle multiple input nodes
• add simplify_neuron function() to make neuron with just one branchpoint
• fix summarise_contributions() for 'synapses' (#34)
• change IVLP -> WED in FAFBNP surfaces (#35)
• fix stitch_neurons() for latest nat 1.9 prerelease (#36)

elmr 0.5

• switch to FAFB14 as the default EM assembly
• provide default objects (FAFB, FAFB.surf, FAFBNP.surf) that will always point to current assembly.
• fix bug in distal_to() (#31)
• doc improvements for distal_to()

elmr 0.4.2

• update to 170303_ELM_landmarks_v14 landmarks (including transforming surfaces)
• first version of unspike() function
• new vignette - making meshes programmatically
• insist on nat >= 1.8.8
• fetchn_fafb()/nblast_fafb() can take pre-downloaded neuronlist
• teach unspike() to keep connectors/soma (#29)

elmr 0.4.1

• Add functions to summarise tracer effort

elmr 0.4

• switch FAFB13-JFRC2013 transform to 170211_new_ELM_landmarks_v7.csv (71 landmarks more evenly spaced on both sides of the brain)
• update FAFB13 and FAFB13NP surface objects accordingly
• fix open_fafb() after change in stack id handling
• add landmarks vignette

elmr 0.3

• make nblast_fafb() parallelised by default
• give open_fafb() arguments for selecting neuron/nodes (#24)
• add FAFB13 brain and neuropil surface objects
• complete switch to FAFB13 assembly (vignettes etc)
• fix open_fafb() for v13 (#23)

elmr 0.2.1

• teach nblast_fafb() to cope with db length <100 (#22)

elmr 0.2

• switch to FAFB13 as default template brain
• much new functionality including transforming between template brains via xform_brain()
• nblast_fafb() for searches

elmr 0.1

• first version

jefferis/elmr documentation built on Sept. 9, 2023, 1:54 p.m.