constantinpape/cluster_tools issues and pull requests

#49 - Avoid deprecated scipy.ndimage sub-namespaces

Pull Request - State: closed - Opened by imagejan 5 months ago

#48 - Always use z5py for zarr files; bump version

Pull Request - State: closed - Opened by constantinpape 6 months ago

#47 - implement metadata checks for downscaling

Pull Request - State: closed - Opened by martinschorb 9 months ago - 3 comments

#46 - `fit_to_roi` not applied

Issue - State: open - Opened by martinschorb 10 months ago

#45 - Pass axis metadata for ome.zarr

Issue - State: open - Opened by constantinpape 10 months ago

#44 - threadpool issue

Issue - State: open - Opened by martinschorb 10 months ago - 11 comments

#43 - dimension slicing error

Issue - State: closed - Opened by martinschorb 10 months ago - 6 comments

#42 - support slicing stacks in arbitrary dimension

Pull Request - State: closed - Opened by martinschorb over 1 year ago - 3 comments

#41 - Update for elf

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

#40 - Input data for axon_dendrite_attribution workflow

Issue - State: open - Opened by daniJb over 1 year ago

#39 - AssertionError: [30, 256, 256], (16, 128, 128

Issue - State: open - Opened by daniJb over 1 year ago - 2 comments

#38 - Replace tail unix command with python impl

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

#37 - Fix issues with uint8 conversion for float data in CopyVolume

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

#36 - Warn for unsafe uint8 conversion

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

#35 - Update copy_volume.py

Pull Request - State: closed - Opened by martinschorb over 2 years ago - 4 comments

#34 - wrong kwarg passed on to elf

Issue - State: closed - Opened by martinschorb over 2 years ago - 17 comments

#33 - Add change from signed int to unsigned int upon copying data

Pull Request - State: closed - Opened by martinschorb over 2 years ago - 12 comments

#32 - Fix downscaling with ome zarr metadata format

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

#31 - Use ome-zarr v04 format and remove bdv.ome.zarr file format

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

#30 - Advanced inference WIP

Pull Request - State: closed - Opened by constantinpape almost 3 years ago - 1 comment

#29 - Enable inference with bioimageio models WIP

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

#28 - Update ilastik prediction workflow

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

#27 - Fix issues with connected components

Issue - State: closed - Opened by constantinpape almost 3 years ago

#26 - Fix tests for edge features

Issue - State: open - Opened by constantinpape about 3 years ago

#25 - Create smaller file for tests

Issue - State: closed - Opened by constantinpape about 3 years ago

#24 - Add prepare_test function and add github CI

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

#23 - Support for cloud-based datastores?

Issue - State: open - Opened by j6k4m8 about 3 years ago - 4 comments

#22 - Use decomposition solver as default for solve_global

Issue - State: open - Opened by constantinpape over 3 years ago

#21 - Block-wise multicut currently does not support halo

Issue - State: open - Opened by constantinpape over 3 years ago

#20 - Store slurm ids as string

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

#19 - Update links for data of LMC publication

Issue - State: open - Opened by constantinpape over 4 years ago

#18 - Axon-Dendrite Attribution code

Issue - State: open - Opened by MatthewBM over 4 years ago - 2 comments

#17 - Update downscaling workflow to support bdv.n5

Pull Request - State: closed - Opened by constantinpape almost 5 years ago

#16 - New graph storage

Pull Request - State: closed - Opened by constantinpape almost 5 years ago

#15 - Implement label multi-set workflow (not fully tested)

Pull Request - State: closed - Opened by constantinpape about 5 years ago

#14 - Migrate functionality to elf

Pull Request - State: closed - Opened by constantinpape over 5 years ago

#13 - Make 'compression' configurable when creating label-to-block-mapping

Pull Request - State: closed - Opened by wolny over 5 years ago

#12 - Add required missing positional argument

Pull Request - State: closed - Opened by wolny over 5 years ago

#11 - Segfault fix in the multicut solver

Pull Request - State: closed - Opened by wolny over 5 years ago - 1 comment

#10 - Sample data doesn't extract

Issue - State: closed - Opened by MatthewBM over 5 years ago

#9 - Updated Learning Workflow to work after name changes

Pull Request - State: closed - Opened by snajder-r over 5 years ago - 1 comment

#8 - How to run large volumes

Issue - State: closed - Opened by MatthewBM over 5 years ago - 21 comments

#7 - Inference workflow

Pull Request - State: closed - Opened by constantinpape over 5 years ago

#6 - Pipeline has problems with non-contiguous numpy arrays

Issue - State: closed - Opened by snajder-r almost 6 years ago - 3 comments

#5 - Pipeline does not work for non-consecutive superpixels

Issue - State: open - Opened by constantinpape almost 6 years ago

#4 - Pipeline does not work with HDF5 input

Issue - State: open - Opened by constantinpape almost 6 years ago

#3 - Tasks do not respect thread limt

Issue - State: closed - Opened by constantinpape almost 6 years ago - 3 comments

#2 - Embl

Pull Request - State: closed - Opened by constantinpape over 6 years ago

#1 - New workflow

Pull Request - State: closed - Opened by constantinpape over 6 years ago

GitHub / constantinpape/cluster_tools issues and pull requests