Scip

22cfb7c Documentation update
f0cf5d4 Update with dynamic amount of output files
6724bad Compute raw unmasked intensity
8c00a36 Dynamic number of output partitions
59f935c Add value range filter and otsu thresholding
b82539b No negative amount of regions when all removed
bc0ff05 Bugfix feature position
9e4de04 Always add regions
ed85449 Update number of regions after filtering regions
0d0a91a Add filters to documentation
618178c Update spot mask
a0a39da Allow empty mask filters config
2900458 Unused import
72cf003 Implement pre mask filters
3d790e5 Switch codecov badge to main
4da0dd8 Update watershed segmentation
5fc3171 Update documentation
ad2d813 Add regex named group sto meta in czi loader
bd714f2 Delay parquet computation
f36d839 Update installation instructions
e8397f4 Bugfix gpu id
05766b7 Add regex to czi meta loader
a1775a8 Add logo to dos
dfa8ff3 Add logo
c12d2a6 Move package data and fix rtd
b533009 Fix indentation
ba1ef4c Switch to markdown
45e89b3 Move config to setup cfg
1c80383 Add cellpose check to main test
a60c0e7 Add cellpose importorskip
c58e1bd Update github actions
e735470 Update dependencies
333a1ee Merge branch 'master' of github.com:ScalableCytometryImageProcessing/SCIP
8aab978 Update pypi info
a23166b Update pypi info

ef26aa6 Update test config
a2097e4 Remove all statement
20b3e2f add all
4e07484 Add minimal dask version
2c36dd9 Style
9f0267b Implement substract mask
900fc3e Bugfix channel index in segmentation
a774b0f Add option for precomputed correction images
2e5100b Fix segment tests
6fed056 Restructure cellpose execution
b74936e Multi channel segmentation
2451995 nbatches to groups
0433e09 Per channel cellpose
57874e9 style enforcement
36e58a7 Documenation update
ae66efd Meta naming
6d161c1 Style enforcement
7c31809 Switch to map partitions
bf36dc2 Merge pull request 52 from ScalableCytometryImageProcessing/refactor
dcabe7e Merge pull request 51 from ScalableCytometryImageProcessing/jones2006
4329213 Fix too complex function + test parameters
4460257 Update test config + noop if downscale is 1
731eeff Add yaml correction settings
4c85b23 Implement scaling to overcome memory issues
e4814c3 Switch median filter functions
d851332 parallelize finish operation
a9e8fe8 Switch to memory efficient but slow medfilt
6d2ec1f Bugfix median filter + deterministic test
546235a Missing keyword
ef0f62b style enforcement
2c6e49c Extend test
fcea8e8 Convert to regular float
6cbedc8 Add minmax test
9115a8e Bugfix nan after correction
b847f2b Bugfixes and add median filter size
d2c3623 Add jones 2006 illumination correction
81bd475 Fix all tests after refactor
49bbd10 Initial refactor
b534057 Make multi mask compatible with other data types
d24d68f Fix example yml config
30a4cc9 Pass smooth parameter as array
98fcfca Add test case
edbe3c9 Move tests to tests folder
45f8d44 Check if edge is foudn
2c9b1ba Remove graph viz
7a704b8 Keep regions
609bd30 Test a number of nbins for threshold minimum
7d5a9c5 Add and test spot mask + update threshold mask
568b902 Rely on unknown divisions
dae366b Update cli test
ccb2547 Add unique id for concatenation + test multi mask
14bd7b2 Initial multi mask implementation
baafc1a Add runtime none check
0c6223f Test cli
646c50b Add oversampling possibility
1b0414e Add limit option to cli
2103d1a Update test with sampling to limit
fd7fff6 Implement limits with random sample from bag
f265f8d Merge branch 'master' of github.com:ScalableCytometryImageProcessing/SCIP
3353676 Add requirement
90386ad Test main function + anndata saving warnings
3a0062b Repartition
3f71c47 Update documentation layout
d41951b Documentation for export module
79768b8 Remove references to report
b9aa65e Skip cellpose if executing on github actions
89ef7cb Remove benchmarking code
43d52c9 Remove dead code

523cc82 - Maxim Lippeveld, 2 minutes ago : Update dask jobqueue
c0d0a2e - Maxim Lippeveld, 5 minutes ago : Update classifiers
f9deb0e - Maxim Lippeveld, 8 minutes ago : Bad identifier
eb1dba1 - Maxim Lippeveld, 54 minutes ago : Change typing signature
b6ca7ab - Maxim Lippeveld, 63 minutes ago : Add init file
500730a - Maxim Lippeveld, 10 days ago : Update czi and tiff tests
e79b9cb - Maxim Lippeveld, 10 days ago : Fix bug when channels are not passed
7e668d5 - Maxim Lippeveld, 10 days ago : Add CZI loading tests
94f54b2 - Maxim Lippeveld, 4 weeks ago : Partition updates and path check
059ed8c - Maxim Lippeveld, 4 weeks ago : Reduce partitions to lower overhead
dbf25a2 - Maxim Lippeveld, 4 weeks ago : Making output optional
1c6ad35 - Maxim Lippeveld, 4 weeks ago : Merge branch 'master' into tiff-seg
fdfc94e - Maxim Lippeveld, 4 weeks ago : Channel order bugfixes
ee13f5b - Maxim Lippeveld, 4 weeks ago : Merge branch 'tiff-seg' into czi-update
33bf048 - Maxim Lippeveld, 4 weeks ago : Merge branch 'tiff-seg' of github.com:ScalableImagingPipeline/dask-pipeline into tiff-seg
f0b8ba4 - Maxim Lippeveld, 4 weeks ago : Wait for workers
767a51d - Maxim Lippeveld, 5 weeks ago : Documentation
5a3105b - Maxim Lippeveld, 5 weeks ago : Export to anndata
36463e5 - Maxim Lippeveld, 5 weeks ago : Updated czi loading to new interface
779d061 - Maxim Lippeveld, 5 weeks ago : flake8 + repartition
0cfddbd - Maxim Lippeveld, 5 weeks ago : Restructure to properly delay loading
17a736e - Maxim Lippeveld, 5 weeks ago : Bugfix delayed call
ea87966 - Maxim Lippeveld, 5 weeks ago : Delay bag from directory
78c475a - Maxim Lippeveld, 5 weeks ago : No more limiting + separate loader meta
a813e69 - Maxim Lippeveld, 5 weeks ago : Update cellpose configuration
853e37b - Maxim Lippeveld, 5 weeks ago : Update tiff test images
15c96bf - Maxim Lippeveld, 8 weeks ago : Use correct block shape dimension
1cc1306 - Maxim Lippeveld, 8 weeks ago : Use type not class
4de8e57 - Maxim Lippeveld, 8 weeks ago : Install with czi dep
0fa7f45 - Maxim Lippeveld, 8 weeks ago : Test tiff bag from directory
7040482 - Maxim Lippeveld, 8 weeks ago : Add tiff loading test + autouse client fixture
5e0d5ae - Maxim Lippeveld, 8 weeks ago : CellPose runs on tiff images
96a97bf - Maxim Lippeveld, 9 weeks ago : Initial implementation
8718491 - Maxim Lippeveld, 3 months ago : Merge branch 'master' of github.com:ScalableCytometryImageProcessing/SCIP
cb75383 - Maxim Lippeveld, 3 months ago : Move jobqueue to extra
6c9b146 - Maxim Lippeveld, 3 months ago : Update README.md
d6943a6 - Maxim Lippeveld, 3 months ago : Merge branch 'cp-updates'
760529c - Maxim Lippeveld, 3 months ago : flake8 compliance
736cc9b - Maxim Lippeveld, 3 months ago : Merge branch 'master' into cp-updates
89e372d - Maxim Lippeveld, 3 months ago : Add zarr testing
f6dc090 - Maxim Lippeveld, 3 months ago : Reparametrize fixtures
38cd1d1 - Maxim Lippeveld, 3 months ago : No need for cluster fixture
3beee05 - Maxim Lippeveld, 3 months ago : Bugfix cellpose mask export
fbcc35d - Maxim Lippeveld, 3 months ago : Make export optional
877897e - Maxim Lippeveld, 3 months ago : flake8
f097fd2 - Maxim Lippeveld, 3 months ago : Exists ok + less annotated tasks
d06517d - Maxim Lippeveld, 3 months ago : Persist + bugfix update mask with nuclei
50e7e91 - Maxim Lippeveld, 3 months ago : Working implementation
be97b09 - Maxim Lippeveld, 3 months ago : Bugfix scene selection
7734aac - Maxim Lippeveld, 3 months ago : Bugfix missing nucleus segmentation
5f81633 - Maxim Lippeveld, 3 months ago : Add more detailed nucleus mask
1906d7e - Maxim Lippeveld, 3 months ago : Merge branch 'master' of github.com:ScalableImagingPipeline/dask-pipeline
50340d1 - Maxim Lippeveld, 3 months ago : lower batch size
8774b31 - Maxim Lippeveld, 3 months ago : Add option to merge adjacent objects after segmentation
97d8d50 - Maxim Lippeveld, 4 months ago : Fix test coverage

9587a24 - Maxim Lippeveld: Move coverage to github workflow
8272cef - Maxim Lippeveld: Update installation with optional dependencies

fd73415 - Maxim Lippeveld, 2 hours ago : Open zarr images read only
2b46cdb - Maxim Lippeveld, 2 hours ago : Update check for hdfs
fac9ea7 - Maxim Lippeveld, 2 hours ago : Remove built docs
7fbbf76 - Maxim Lippeveld, 2 hours ago : Change path type to str to allow (hdfs) urls
1c288c4 - Maxim Lippeveld, 20 hours ago : Add some comments to yaml config
e253d32 - Maxim Lippeveld, 3 days ago : Add usage info
f829c85 - Maxim Lippeveld, 10 days ago : Correctly handle empty combined indices
ad28509 - Maxim Lippeveld, 11 days ago : Add external mode for connecting to existing cluster
afb48d5 - Maxim Lippeveld, 13 days ago : Add codecov badge
2602a20 - Maxim Lippeveld, 13 days ago : Document data loading modules
049f74c - Maxim Lippeveld, 2 weeks ago : pytest
b7f83e1 - Maxim Lippeveld, 2 weeks ago : Add codecov
f0866c9 - Maxim Lippeveld, 2 weeks ago : flake8
a4559e6 - Maxim Lippeveld, 2 weeks ago : Coverage configuration, add fixtures, fix quantile tests
cebd70c - Maxim Lippeveld, 2 weeks ago : Add feature extraction test
9bb1f6c - Maxim Lippeveld, 3 weeks ago : configure channel in combined mask
907cd5b - Maxim Lippeveld, 3 weeks ago : Start with main channel
f094440 - Maxim Lippeveld, 3 weeks ago : Correctly report number of workers

909417b - Maxim Lippeveld: Update czi dependency
b2ea1cf - Maxim Lippeveld: Allow scenes to be selected with regex
72c0767 - Maxim Lippeveld: Fix bounding box bug + update test