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

New Contributors

• @nf-core-bot made their first contribution in https://github.com/nf-core/molkart/pull/1
• @FloWuenne made their first contribution in https://github.com/nf-core/molkart/pull/2

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