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BioinfoTongLI merged 136 commits intocellgeni:developcellgeni/modules:developfrom BioinfoTongLI:developBioinfoTongLI/modules:developCopy head branch name to clipboardMar 18, 2025

Commits

Commits on Nov 8, 2024

• minor fix

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  2890d00

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• Merge branch 'master' into develop

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  6167e30

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• yet another bad simple quote

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• use workdir for model caching

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  f812f71

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• minor fix

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  e953425

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• bump version; use tiffilfe for chunk access

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• default to /models for external data

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Commits on Nov 14, 2024

• init spatialdata parallel query

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  aa06ba0

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• minor debug

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  8b0da56

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• give correct output names to cropping step

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  4733f86

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• use path for folders

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• handle specific case when partition is 1

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  5928d8d

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Commits on Nov 20, 2024

• init commit

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  a0c03ac

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• rename properly

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  dd33e4c

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• working version

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  2e1d23d

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• add metadata description for the task

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  e5cf055

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Commits on Nov 21, 2024

• init commit for fractal cellpose

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  ebc7755

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Commits on Nov 28, 2024

• bump version to 0.0.2

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  8a28283

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• state python path explicitely

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  c54c6d2

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Commits on Nov 29, 2024

• bump version to 0.5.1 and include model into /models/

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  ea39c83

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• requires double quote

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• hard copy the model into the dir; discard user options

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  37cd0b0

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Commits on Dec 5, 2024

• refactored; nf-test passed

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  3a71677

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• added tests; save pretrained models into docker; user resources folder

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  4dad5b5

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• delete tiled_stardist

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  c174512

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• minor refact for nf-core

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  f1e2272

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Commits on Feb 2, 2025

• update meta yam for generatetiles

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  214c092

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• updated meta yaml for fractal cellpose

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  6de1648

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• add mergeoutline module binary and nextflow.config

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  1be4db9

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• update cellpose test file

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  8591409

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• update test files to zarr

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  d070dfd

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• add zarr for mergeoutlines

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  6263dc3

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• update tiled segmentation subworkflow

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  dd7a3f8

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• add mergeoutlines module

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  80b6240

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Commits on Feb 3, 2025

• added test for stardist

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  cca2bf7

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• add stardist helper script

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  3c27dea

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• update

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• ignore for now

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  7f2755f

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• use the same output channel name between cellpose and stardist

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  2b3c7fc

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• update channel value order

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  cc4b26e

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• update test

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  36da187

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• add testing specific config file

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  591f172

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• update test config. Somehow it hangs forever.

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  0587794

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• added stardist option for the subworkflow

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  6714573

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• update mergeoutlines along with tests

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  824bf32

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• nf-test hangs

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  3d1cdf3

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• use the nf-version of MERGE_OUTLINES

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  779331b

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• remove local test files

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  813193d

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• do not pass cell diameter to the output channels

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  a8ec6a9

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• minor bug fixing

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  774b7a3

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• update stardist test snap

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  2148abe

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Commits on Feb 6, 2025

• init push for instanseg with tests

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  291d154

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• meta.yaml for describing the module IO and empty conda env

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  b04e7d6

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• add default testdata_base_path

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  5ea91da

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• added multiple instance test, but hands forever. Added instanseg

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  e4e2765

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• update minor issue with wkt

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  f930573

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• update cellpose tests and added stub section

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  331a080

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• added stub adn updated unittests.

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  2458057

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• update gitignore

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  ce72cc7

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• add test unittest for spotiflow module

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  f6c60fa

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• added exectable scripts to the module

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  e9d1f21

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• bump container version to 0.5.2

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Commits on Feb 7, 2025

• Merge branch 'cellgeni:develop' into develop

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  f582efd

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• removed irrelevant scripts and slightly updated the script

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  8285b83

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• update test snap accordingly

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  db1c37b

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• better variable handling in the process

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  f161d25

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• minor cleanup and update tests

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  9997ed2

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• slight simplification

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  7bca20f

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• added the module to merge peaks in csv files and output a wkt multipoint file

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  b11ad60

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• add concatenate peaks

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  38765ad

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• switch to module based solutions

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  efbfb40

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• added tests for mergeoutlines

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  c2f4a80

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• added deepcell module

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• added deepcell and tests into subworkflow. But the test run hangs

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Commits on Feb 10, 2025

• add GPU labels for segmentation tools

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  2ac840e

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• fix typo

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  e765ea0

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• handle empty detection

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  68bf0cb

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• make the output unique

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Commits on Feb 11, 2025

• update deepcell test snap

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  42995c9

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• update instanseg test snap

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  b588f12

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• update stardist test snap

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• use default to tiffile's lazy chunk loading; add more tracable output name

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  82babde

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• use lazy tile loading for deepcell

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  a29e2b2

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• trying to fix the issue when the largest polygon is of area 0(?)

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  5e4a23a

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• update postcode to latest; tests don't work yet

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Commits on Feb 12, 2025

• add the merfish solution back

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Commits on Feb 14, 2025

• reject invalid polygons before merging.

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  ac0c5cc

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• fix stupid typo cropping images

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  37fe963

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• fix that stupid error again...

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  cf9acaa

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• once again

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Commits on Feb 16, 2025

• avoid returning none

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  56cc9fa

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• grouple Tuple using meta channel only

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  d537101

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Commits on Feb 18, 2025

• apply baseline translation for each tile.

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  878d03b

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Commits on Feb 27, 2025

• externalised get_tile func and bumped cellpose_seg version

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• do not enforce gpu tag. Otherwise cannot switch to cpu queues.

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  7d65e75

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• update the get tile lib to handle microaligner edge case

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  ea16336

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• externalised the whole image parsing

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  dc4cf77

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• use image cropper to get the tile

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  b057442

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• bump spotfilow wrapper version and update test.

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  2b9b97d

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• update test snap

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  98083d5

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• remove ch_ind in meta to faciliate downstream grouping

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• groupby meta without ch_ind

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  fd1c15c

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Commits on Mar 3, 2025

• update test snap; explicite write xmin/max and ymin/max in the output file name

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• do not remove ch_ind in peak-calling step

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Commits on Mar 4, 2025

• add back the line for incorporating ch_ind into meta

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  93e7f82

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• use a dedicated channel for channel index

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  157967f

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• update cropper to pass through the channel index

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  9b3ebce

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• update spotiflow and the container

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  e41f0d8

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Commits on Mar 14, 2025

• do not use local img-cropper. use the imagetileprocessor to fetch tiles

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  ca029aa

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• use imagetileprocessor; bump test snap

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  2be815f

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• update test snap

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  c8535dc

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• switch to imagetileprocessor

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  ba15989

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• update deepcell container version

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  514d8b0

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• use imagetileprocessor with instanseg

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  4c3b881

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• update instanseg container; remove gpu label

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  dd8bf53

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• use imagetileprocessor with stardist helper

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Commits on Mar 15, 2025

• better naming conversion to keep origianl tool version

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  acb6d51

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• update merge peaks

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  68300d4

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• switch to imagetileprocessor

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  a2a35af

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• bump container version

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  5f5a2c7

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• use exectuable in imagetileprocessor for mergeoutlines; cleanup; update snap

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  d0f2372

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• add copy right

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  ff9d1d9

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• major update of PoSTcode

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  e0042a7

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• properly map barcode for both merfish-like and iss-like methods

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  bfb8c4a

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• handle minor exception

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  2cea5bd

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Commits on Mar 16, 2025

• default to geojson for merged segmentation

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  86fb3ef

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• minor fix for microaligner output

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  da6205d

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• better way of passing ext.args to test cases

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  2176596

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Commits on Mar 18, 2025

• use imagetileprocessor to do the merging

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  b49455c

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• switch to imagetileprocessor and bump software version

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  866ca82

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• update test snap file

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  1b84367

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• remove the local script

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  e8b4172

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• remove hard gpu label, since it will bug when gpu is absent

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  cd4b39b

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• make sure images are of class channel inside the subworkflow

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  ac4cefc

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• save multipolygon as the other methods

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  a648be3

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• used workflow snapshot instead of process; removed stub

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