Spatial Circuit

This is the first release of molkart.

In this version, provided nuclear image data can be preprocessed, with second image inputs supported. Three image-based segmentation tools are available as segmentation options and masks can be filtered. Previously called spots (provided as input) are filtered and assigned to cells based on the segmentation masks and quantified, with appropriate QC metrics returned. Additionally, crop creation for training segmentation models (after preprocessing) is supported. Final output is an AnnData object in SquidPy format.

What's Changed

• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #1
• First minimal working version of pipeline by @FloWuenne in #2
• Important! Template update for nf-core/tools v2.10 by @nf-core-bot in #3
• Initial setup by @kbestak in #4
• Initial MultiQC parsing by @kbestak in #10
• Replaced clahe param with the skip_clahe param by @kbestak in #14
• Replacing PROJECT_SPOTS and MCQUANT by more optimized method by @FloWuenne in #15
• Added tilesize parameter for mindagap and mindagap_duplicatefinder by @kbestak in #18
• Documentation by @kbestak in #19
• Cellpose fix - custom model and multiple samples by @kbestak in #20
• Added nf-test for pipeline main.nf by @kbestak in #25
• Mindagap outputs by @kbestak in #30
• CLAHE changes by @kbestak in #31
• Replaced local mindagap/duplicatefinder with nf-core module. by @FloWuenne in #32
• maskfilter added, molkartqc update, prefix fix, versions by @kbestak in #33
• Local module revamp by @kbestak in #35
• Crop overview multiqc by @kbestak in #36
• Added full test config file. by @FloWuenne in #39
• Speedup mask filter. by @FloWuenne in #40
• Clahe prefix fix by @FloWuenne in #42
• Fixed bug in Maskfilter config. by @FloWuenne in #45
• Process resources by @FloWuenne in #44
• Template update for nf-core/tools version 2.11.1 by @kbestak in #48
• Important! Template update for nf-core/tools v2.11 by @nf-core-bot in #46
• Added anndata as an output format by @FloWuenne in #49
• Molkart local fix by @FloWuenne in #50
• Molkartqc hotfix by @FloWuenne in #51
• Module update + CI by @kbestak in #52
• updated mesmer to exlude leftover todo by @kbestak in #53
• PR for first release by @kbestak in #54

New Contributors

• @nf-core-bot made their first contribution in #1
• @FloWuenne made their first contribution in #2

Full Changelog: https://github.com/nf-core/molkart/commits/1.0.0