Jun Sung Park

Dear @BALuca and Ecotyper team, Hi, all! Thank you so much for sharing great tool with community. I come across with same error with @NoahHenrikKleinschmidt using self-built singularity image. I...

Hi, @grst @redst4r Thank you for sharing great wrapper for infercnvpy. I've been trying to annotate matching gene on heatmap plot (c.f., bottom for all/subset of matching gene symbols) but...

Hi, @quentinblampey! I also happen to come across need extra baysor information (e.g., confidence score) to filter out cells containing low quality transcripts to achieve better annotation. Any chance that...

Hi, @EliHei2! Many thanks for suggestion. I followed your attached script and come across with following error that I couldn't resolve yet. Any chance you notice it before on current...

Hi, @EliHei2! Thank you so much for updating the scripts. seg2explorer seems running this time with those codes but come across with following error: ########################################################### from segger.validation.xenium_explorer import seg2explorer import...

(Update) It seem even though `seg2explorer` failed, `segger_cell_boundaries.parquet` generation is working with the corrected scripts. One burning question is, as morphology image and boundary image are having different orientation and...

FYI, I got the same error as @erkinacar5 while running following (5k panel; Xenium v2 with multiple sections): ################################################################################################# import dask.dataframe as dd ddf = dd.read_parquet('/project/simmons_hts/jpark/0_tools/segger_dev/data_segger/RUNTRexBio_SLIDE1/benchmarks/segger_output_0.5_False_4_12_15_3_20250730/segger_transcripts.parquet').compute() ddf = ddf.dropna() ddf...