Vladislav Vlasov

icon indicating a website link vsco.co/hey2homie

icon company VUB icon location Antwerp, Belgium icon location Bioinformatician at BSIL-BCIM VUB. Spatial proteomics, data science and CV. Shooting film on weekends.

Results 4 comments of Vladislav Vlasov

Add option not to fill masks. Compression to TIFF files.

Sure, this usually gets quite prominent with the ramified glia cells like on this two crops (left is grey-scale, right are masks with holes): ![holes_examples](https://github.com/MouseLand/cellpose/assets/54250636/5f945a76-867c-47b4-9752-7609f008d370) I've also added the possibility...

Add option not to fill masks. Compression to TIFF files.

@mrariden, I've also added options to fill in holes that are less than certain threshold. I've also added in the same PR option to save masks with/without holes in `geojson`...

Add option not to fill masks. Compression to TIFF files.

Here is example of plotted outlines: ![example_1](https://github.com/MouseLand/cellpose/assets/54250636/b56ae18f-fe84-4049-bc20-a7dfbf977641) ![example_2](https://github.com/MouseLand/cellpose/assets/54250636/8ed85e9a-efd1-4fa6-8af7-288a6a86c134) Time it takes to save `tiff`, write coordinates and plot outlines for a single mask 512 by 512: * Before ``` 2024-03-21...

Faster implementation available for `vectorize()`

@LucaMarconato, thanks for reaching out! Was a bit busy lately to follow-up on this. There were some minor issues in the code from the hackathon, but I've already fixed them....