Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ScalableCytometryImageProcessing/SCIP issues and pull requests

#53 - Is this pipeline actively maintained?

Issue - State: open - Opened by tatyana-perlova 10 months ago - 1 comment

#52 - Refactor

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

#51 - Jones2006 illumination correction

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

#50 - Use pre-commit package for enforcement

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

#49 - Export to AnnData for interoperability with ScanPy

Issue - State: closed - Opened by MaximLippeveld over 2 years ago
Labels: enhancement

#48 - Specify different memory requirements for GPU workers in mpi mode

Issue - State: open - Opened by MaximLippeveld over 2 years ago
Labels: enhancement

#47 - Implement possibility to refine masks after CellPose segmentation

Issue - State: open - Opened by MaximLippeveld almost 3 years ago - 1 comment
Labels: segmentation

#46 - For large datasets, SCIP hangs when exporting features

Issue - State: closed - Opened by MaximLippeveld almost 3 years ago
Labels: bug, image-features

#45 - Create LICENSE

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

#44 - Switch to tifffile in multiframe tiff loader

Issue - State: open - Opened by MaximLippeveld about 3 years ago
Labels: data-loading

#43 - Update masking for IFC data

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: segmentation, image-features

#42 - Segmentation of optical microscopy images

Issue - State: closed - Opened by MaximLippeveld about 3 years ago - 1 comment
Labels: segmentation

#41 - Focus selection or focus stacking for multi-focal images

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: preprocessing

#40 - Support for CZI images

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: data-loading

#39 - Export mask bounding box

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: segmentation

#38 - Better basic mask quality control

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: segmentation

#37 - Export to AnnData

Issue - State: closed - Opened by MaximLippeveld about 3 years ago - 1 comment
Labels: enhancement, wontfix

#36 - Switch to async cluster for benchmarking

Issue - State: closed - Opened by MaximLippeveld about 3 years ago - 1 comment
Labels: enhancement, wontfix

#35 - Add fluorescence intensity quality control plots to spot batch effects

Issue - State: open - Opened by MaximLippeveld about 3 years ago
Labels: preprocessing

#33 - Crop images to bounding box of mask to reduce computation and storage overhead

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: enhancement, preprocessing

#32 - Add CellProfiler granularity features

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: image-features

#31 - Fix hog features

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: bug, image-features

#30 - Render reports using Jinja template engine

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: enhancement

#29 - Rewrite reporting and exporting flow

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: enhancement

#28 - Add per-sample min-max normalization

Issue - State: closed - Opened by MaximLippeveld about 3 years ago
Labels: preprocessing

#27 - Compute quantiles with random undersampling

Issue - State: open - Opened by MaximLippeveld about 3 years ago
Labels: preprocessing

#26 - Add per-image min-max normalization

Issue - State: open - Opened by MaximLippeveld about 3 years ago
Labels: preprocessing

#25 - Move UMAP to separate module

Issue - State: closed - Opened by MaximLippeveld about 3 years ago - 1 comment
Labels: analysis

#24 - Add Local Binary Pattern texture features

Issue - State: closed - Opened by MaximLippeveld about 3 years ago - 1 comment
Labels: image-features

#23 - Implementation of distributed Fuzzy C-means

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 1 comment
Labels: enhancement

#22 - Export intensity distribution reports to HTML instead of PDF

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: enhancement

#20 - Smart indexing on Dask Dataframe

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 1 comment
Labels: enhancement

#19 - Dimensionality reduction after feature extraction

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 1 comment
Labels: enhancement

#18 - Benchmark/use DoG instead of Non-local means denoising in mask segmentation

Issue - State: closed - Opened by sanderthierens over 3 years ago
Labels: segmentation

#17 - Benchmarking scalability of data loading + masking

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: documentation

#16 - Use CellProfiler to extract features

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 1 comment
Labels: enhancement, image-features

#15 - Support for other microscopy formats through Bio-Formats

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 2 comments
Labels: enhancement, wontfix, data-loading

#14 - Channel normalisation

Issue - State: closed - Opened by sanderthierens over 3 years ago - 2 comments

#13 - Implement principal feature analysis

Issue - State: open - Opened by MaximLippeveld over 3 years ago
Labels: enhancement, image-features

#12 - Implement feature extraction that combines channels

Issue - State: open - Opened by MaximLippeveld over 3 years ago
Labels: enhancement, image-features

#11 - Perform background subtraction

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 3 comments
Labels: enhancement, segmentation

#10 - Add info and debug logging statements

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: enhancement

#9 - Feature extraction quality control report

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: enhancement, image-features

#8 - Feature extraction from pretrained neural nets

Issue - State: open - Opened by MaximLippeveld over 3 years ago
Labels: enhancement, image-features

#7 - Add unit tests

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: enhancement

#6 - Masking quality control report

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: enhancement, segmentation

#5 - Image normalization after masking

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 1 comment
Labels: enhancement, segmentation

#4 - Alternative segmentation for noisy channels

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 1 comment
Labels: bug

#3 - Add pipeline and run configuration

Issue - State: closed - Opened by MaximLippeveld over 3 years ago
Labels: enhancement

#2 - Start new module for feature extraction

Issue - State: closed - Opened by MaximLippeveld over 3 years ago - 3 comments
Labels: enhancement, image-features

#1 - Add demo dataset for new users

Issue - State: open - Opened by MaximLippeveld over 3 years ago
Labels: enhancement