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.