cytokit

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MySQL Error - Improve Selection of plane

2

Hi Eric, I have started to see the following error with regard the MySQL database  Also I have notice that the software is saving the wrong planes to display...

jesusdpa1

Difficulties running cytokit on codex data

6

Hi, I am trying to run cytokit on our acquired data, but I am not able to set up the ylam correctly nor the processing bash file. we ran 9...

jesusdpa1

Make example data sets public

3

Here are the ones that we are familiar with and trust the most: ```bash $ gsutil ls gs://musc-codex/datasets/ \ | grep "20180706\|20180614" \ | xargs -I@ -P1 bash -c "gsutil...

armish

Some preliminary notes: # Cytokit on gcloud Spin up a machine on gcloud: 2 GPUs Nvidia K80 ```bash gcloud beta compute \ --project=hammerlab-chs \ instances create \ cytokit \ --zone=us-east1-c...

armish

Segmentation Methodology

1

Relevant section from the [CODEX preprint](https://www.biorxiv.org/content/early/2018/02/05/203166): > A 3D segmentation algorithm was therefore created to combine information from the nuclear staining and a ubiquitous membrane marker (in this case CD45)...

eric-czech