Sébastien Dumas

Hi Seppe, Here is the code I run in R to build and save the model ```r #create cistopic object cisTopic_obj

Here is what I get: ``` >>> print(model) CistopicLDAModel with 45 topics and n_cells × n_regions = 4900 × 346902 >>> vars(model) {'metrics': None, 'coherence': None, 'marg_topic': None, 'topic_ass': None,...

OK, I'm doing it. So far it seems to run properly (see below). It didn't get stuck at the first steps as when using multiple cores. ``` >>> run_pycistarget( ......

It finished properly using 1cpu in 2 hours. So it is probably an error only occurring with the parallelisation. Is there anything I could test to troubleshoot ? ``` 2023-08-09...

Hi @SeppeDeWinter , Following up on this topic ;) : considering I already have performed DAR analysis in Signac, do you suggest to rerun these analyses with pycisTopic ? or...

Hi, I have the same issue as @yolcasmar Do you have any fix? Thank you ! Sébastien

Example of error I get for "otsu" (I have the same error for "3k" unless I set plot to False): region_bin_topics_otsu = binarize_topics( cistopic_obj, method='otsu', plot=False, num_columns=5) --------------------------------------------------------------------------- ValueError Traceback...