Nils Eling

Reading in segmentation masks with missing object IDs

1

**Describe the bug** As an example I generated a segmentation mask (unsigned 16-bit) with missing object IDs. Missing object IDs were induced by shrinking object before resizing them. In any...

Comparison of neighbour detection to CellProfiler

5

Hey, I came around to test the similarity between the CellProfiler neighbour detection approach (mask expansion) to `steinbock measure neighbors --type expansion --dmax `. This is just for documentation purposes...

Feature request: saving images in other file formats

5

This is more to track a discussion: Would you consider supporting the storage of images in other file formats, e.g. .h5? I'm just asking since `cytomapper` could directly link to...

Make image handling more efficient

11

Somehow use raster images to write .h5 files - basically avoiding loading images into memory

- [ ] set `normalize` as generic - [ ] move `EBImage` from Depends to Exports

Build a new data class for Bioconductor

As discussed with @ellispatrick it might be good to add a function that reads in single-channel tiffs into multi-channel CytoImageList objects. In general this is the format often used to...

Make sure that regex matching is only applied to filenames, not paths

Switch to snapshot unit testing

1

We need to wait until the `expect_snapshot_output` of the `testthat` package makes it on CRAN.