Ecosyste.ms: Issues

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GitHub / seung-lab/chunkflow issues and pull requests

#306 - Various fixes and improvements to the save-zarr command

Pull Request - State: open - Opened by eschombu 2 months ago

#305 - Outdated inference.sh script in the examples

Issue - State: open - Opened by wzz332 4 months ago

#304 - fix: update viewer to new microviewer dependency

Pull Request - State: closed - Opened by william-silversmith 8 months ago
Labels: bug

#303 - fix load_png_images to use bounding box starts & stops

Pull Request - State: closed - Opened by eschombu 11 months ago - 1 comment

#302 - add 1-dim probability map shader to chunkflow neuroglancer command

Pull Request - State: closed - Opened by eschombu 11 months ago - 1 comment

#301 - fix volume_size param in create-info command for multichannel case

Pull Request - State: closed - Opened by eschombu 11 months ago - 1 comment

#299 - BoundingBox.decompose fix (plus some other minor changes)

Pull Request - State: closed - Opened by eschombu about 1 year ago

#298 - skeleton visualization in neuroglancer is not working

Issue - State: open - Opened by jingpengw about 1 year ago

#297 - switch to zarr

Issue - State: open - Opened by jingpengw about 1 year ago

#296 - load skeleton operator

Pull Request - State: closed - Opened by jingpengw about 1 year ago

#295 - Fastapi

Pull Request - State: closed - Opened by jingpengw over 1 year ago

#294 - Shrink operators, remove cloud-watch to plugin

Pull Request - State: closed - Opened by jingpengw over 1 year ago

#293 - add skip-task-by-blocks-in-volume

Pull Request - State: closed - Opened by jingpengw over 1 year ago

#292 - additional static layer in neuroglancer

Issue - State: open - Opened by jingpengw over 1 year ago
Labels: enhancement

#291 - [feature] skip existing chunks in a precomputed volume

Issue - State: closed - Opened by jingpengw over 1 year ago - 1 comment
Labels: enhancement

#290 - Test time augmentation

Pull Request - State: closed - Opened by jingpengw over 1 year ago

#289 - napari viewer operator

Pull Request - State: closed - Opened by jingpengw over 1 year ago

#288 - remove the inheritance of Bbox from CloudVolume

Issue - State: closed - Opened by jingpengw almost 2 years ago - 1 comment

#287 - refactor volume

Pull Request - State: closed - Opened by jingpengw almost 2 years ago

#285 - move rarely used operators to plugins

Issue - State: open - Opened by jingpengw about 2 years ago

#284 - rename bbox to roi

Issue - State: open - Opened by jingpengw about 2 years ago

#283 - Test time augmentation

Pull Request - State: closed - Opened by jingpengw about 2 years ago

#282 - add load zarr plugin

Pull Request - State: closed - Opened by jingpengw about 2 years ago - 1 comment

#281 - feat: allow inference beyond mip 3

Issue - State: open - Opened by macrintr about 2 years ago - 1 comment

#280 - Load mrc

Pull Request - State: closed - Opened by jingpengw over 2 years ago

#279 - reading using tensorstore is working

Pull Request - State: closed - Opened by jingpengw over 2 years ago

#278 - perform IO using tensorstore

Issue - State: closed - Opened by jingpengw over 2 years ago - 1 comment

#277 - [Feature] async patch provider

Issue - State: open - Opened by jingpengw over 2 years ago

#276 - Test time augmentation

Pull Request - State: closed - Opened by jingpengw over 2 years ago

#275 - support IO of Zar format

Issue - State: closed - Opened by jingpengw almost 3 years ago - 2 comments

#274 - Need the dependency pandas<1.4

Issue - State: closed - Opened by JackieZhai almost 3 years ago - 2 comments

#273 - input-patch-size etc in setup_env

Issue - State: closed - Opened by ranlu almost 3 years ago - 3 comments

#272 - add operator of download-mesh

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#271 - bounding box coordinate could be switched!

Issue - State: closed - Opened by jingpengw almost 3 years ago
Labels: bug

#270 - [enhancement] skip tasks with file lock

Issue - State: open - Opened by jingpengw almost 3 years ago

#268 - change some default options, add option for test_time augmentation.

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#267 - perf: faster PNG encode/decode

Pull Request - State: closed - Opened by william-silversmith almost 3 years ago

#266 - Crop bbox

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#265 - fix generate tasks when there is no input chunk

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#264 - use python 3.8 for doc building

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#263 - make ci work; upgrade to pandas 1.4.0

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#262 - Post

Pull Request - State: closed - Opened by jingpengw almost 3 years ago

#261 - Postsynapse

Pull Request - State: closed - Opened by jingpengw about 3 years ago - 1 comment

#260 - [feature] remove duplicated points in synapses

Issue - State: open - Opened by jingpengw about 3 years ago - 1 comment

#259 - fixed a bug of post_synapse physical coordinate; rename tbars to pres…

Pull Request - State: closed - Opened by jingpengw about 3 years ago

#258 - detect T-bars and ingest to DVID server

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#257 - [feature] a plugin to visualize all the point cloud of T-bar detection

Issue - State: closed - Opened by jingpengw over 3 years ago - 1 comment

#256 - [inference error] crop output patch and mask the output chunk

Issue - State: closed - Opened by jingpengw over 3 years ago - 1 comment

#255 - Fix threshold type

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#254 - add new operator read-json; adapt to new synapse json format

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#252 - 命令错误

Issue - State: closed - Opened by genggeng-123 over 3 years ago - 5 comments

#251 - Merge segmentation neighbor

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#249 - add neighbors property for bounding box

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#248 - add zero filling option for read-h5 operator

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#247 - fix plugin path

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#246 - create an empty file when we skip the task

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#245 - Logo

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#244 - skip tasks with existing result file; skip task with all zero chunks

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#242 - fix unit tests; add gaussian filter operator

Pull Request - State: closed - Opened by jingpengw over 3 years ago

#241 - Neuroglancer synapses

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#240 - update documentation and tutorial

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#239 - move agglomerate from operator to plugin to remove dependency of waterz.

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#238 - move waterz as a plugin

Issue - State: closed - Opened by jingpengw almost 4 years ago - 2 comments

#237 - current task index and total task number in global states

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#236 - add properties to synchronize the properties consistently and easy to…

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#235 - Aligned tasks

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#234 - write pngs with z coordinate as file name

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#233 - Broadcast mip

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#232 - new operators to read and write Nrrd file

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#231 - Broadcast mip

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#230 - Quit neuroglancer

Pull Request - State: closed - Opened by jingpengw almost 4 years ago

#229 - Better generate tasks

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#228 - make masking work for 3D downsampled masks

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#227 - plugin with bounding box and arguments

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#226 - automatically add voxel offset and voxel size for chunks

Pull Request - State: closed - Opened by jingpengw about 4 years ago - 1 comment

#225 - Fix bugs

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#224 - chunk inherit from np.ndarray

Issue - State: closed - Opened by jingpengw about 4 years ago

#223 - autocomplete of command line

Issue - State: open - Opened by jingpengw about 4 years ago - 1 comment

#222 - test time augmentation in convnet inference

Issue - State: closed - Opened by jingpengw about 4 years ago - 1 comment
Labels: enhancement

#221 - fix connected components

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#220 - make voxel_offset to be 3D

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#219 - downsample in 3D and mask out chunks

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#218 - add voxel size option for chunk class

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#217 - Downsample factor

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#216 - make manifest work

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#215 - fix plugins test; use sharded mesh instead of separated mesh;

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#214 - accept multiple data types in the plugin operator, such as bounding box.

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#213 - remap operator works

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#212 - add disbatch option for generate tasks and use the environment variable

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#211 - use python logging module to replace verbose parameter

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#210 - make create-info operator works with reading and can create precomput…

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#209 - update version

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#208 - rename several operators to make them more consistent

Pull Request - State: closed - Opened by jingpengw about 4 years ago

#207 - [feature] support hierarchical downsampling in Z axis

Issue - State: closed - Opened by jingpengw about 4 years ago - 1 comment