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hammerlab / cytokit

Microscopy Image Cytometry Toolkit
Apache License 2.0
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MySQL Error - Improve Selection of plane #22

Open jesusdpa1 opened 4 years ago

jesusdpa1 commented 4 years ago

Hi Eric,

I have started to see the following error with regard the MySQL database

image

Also I have notice that the software is saving the wrong planes to display and probably it is because I am choosing the incorrect parameters at the config files (posted below).

image

pipeline_execution.txt explorer_config.txt experiment.txt

Moreover, I would like to run deconvolution. For this I should set the wavelengths to each of the markers, for example: DAPI=488 or the time of exposure 1/10

eric-czech commented 4 years ago

Hm I'm not sure about the plane selection without knowing more about in what that isn't what you expect.

Are you using CP Analyst to analyze the exports? If not, set cellprofiler_quantification.export_db to False to disable that sqlite export entirely (the CP code is calling it a MySQL error but that isn't true in this case). If you are, then is it open and pointed at the sqlite db when you're running this? That might cause the lock, but I'm not sure what else would. Either way, deleting everything under $output_dir/$variant/cytometry/cellprofiler and running again may help.

The wavelengths for deconvolution should be the emission wavelengths for the channels in nanometers (no information about exposure is necessary).

cellprofiler_quantification

jesusdpa1 commented 4 years ago

Hi Eric,

With regard of the NN, I was not choosing the correct explorer settings. Overall this step is behaving as expected selecting the best plane and doing the segmentation.

After changing the settings for the cellprofiler I started getting the following error:

image