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molkart-local / MolkartGarage

Repository for local modules used in nf-core/molkart - https://nf-co.re/molkart/dev.

The purpose of this repository is to have one place to manage local modules for molkart mostly in the context of Docker images, as their functionalities are either overlapping or basic so it is possible to include more tools in one image.

Included scripts:

Contrast-limited adaptive histogram equalization (CLAHE)

  • molkart_clahe.py - Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.\
Argument Required Default Value Description
--input Yes N/A File path to input image.
--output Yes N/A Path to output image.
--cliplimit Yes 0.01 Clip Limit for CLAHE.
--kernel No 25 Kernel size for CLAHE.
--nbins No 256 Number of bins for CLAHE.
--pixel-size No N/A Image pixel size.
--tile-size No 1072 Tile size for pyramid generation (must be divisible by 16).
--version No 0.1.1 Print version and exit

Spot2cell - Transcript assignment to cell labels

  • molkart_spot2cell.py - matches a spot table to a segmentation mask to produce a cell-by-transcript matrix.
Argument Required Default Value Description
--spot_table No N/A Spot table to project.
--cell_mask No N/A Sample ID.
--output No N/A Output path.
--version No 0.1.1 Print version and exit

Maskfilter - Filter segmentation masks by area

  • molkart_maskfilter.py - takes a segmentation mask and filters cells based on area from the mask.
Argument Required Default Value Description
--input Yes N/A File path to input image.
--output Yes N/A Path to output image.
--output_qc No N/A Path to output qc csv file.
--min_area No None Lower area (in px) threshold for cell removal.
--max_area No None Upper area (in px) threshold for cell removal.
--version No 0.1.1 Print version and exit

Other scripts

  • molkart_crophdf5.py - converts input to hdf5 and creates crops and a CropOverview.
  • molkart_croptiff.py - creates tiff crops based on a provided CropOverview (To be adapted)
  • molkart_stack.py - takes multiple input images and concatenates them to a stack - pyramidal output. (channel names not preserved)
  • molkartqc.py - gathers provided quality control metrices and gathers them into one csv file.