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choosehappy / HistoQC

HistoQC is an open-source quality control tool for digital pathology slides
BSD 3-Clause Clear License
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UI: CorhortFinder issues #241

Closed nijunnijun closed 1 year ago

nijunnijun commented 1 year ago

After clicking on CorhortFinder, it opens up file explorer. What file should I select here? I tried results.tsv but nothing happened. BTW, Instruction button is not working. Is there user guide some where? Also, do you have a recommended browser? I tried both Edge and Chrome but the UMAP doesnt seem to display correctly.

choosehappy commented 1 year ago

results.tsv is the correct file. i have always used chrome with great success. I'm hoping @nanli-emory can help you out?

nanli-emory commented 1 year ago

Hi @nijunnijun, Do you mind if you can share your results.tsv file with me?

nijunnijun commented 1 year ago

image results.zip Hi @nanli-emory, I am attaching the results.tsv and a screenshot to show nothing happens after selecting this file in the CorhortFinder. Is there a separate repo I need to download for the finder? Thanks.

nanli-emory commented 1 year ago

Hi @nijunnijun, The results.tsv that you shared was generated by HistoQC. You have to use this file as input file to run CohortFinder. The CohortFinder will generate a new results_cohortfinder.tsv files. You have to select the results_cohortfinder.tsv file after you click on CorhortFinder btn.

results_cohortfinder.tsv should include cluster info.

workflow should be:

  1. run HistoQC and generate results.tsv (1) files.
  2. run CohortFinder and use HistoQC's output as CohortFinder's input to generate results_cohortfinder.tsv(2)
  3. run HistoQC.UI and load results.tsv(1), select the results_cohortfinder.tsv(2) file after clicking on CorhortFinder btn

Hi @choosehappy, please correct me if my understand of the workflow is incorrect.