Color Depth MIP Search Tools

This is a set of tools for precomputing color depth searches using the same algorithms as ColorMIP_Mask_Search Fiji plugin. The precomputed results are persisted in a Mongo database and can be exported to JSON in order to upload them to AWS for NeuronBridge.

Build

./mvnw install

or just

./mvnw package

Build the docker container

docker buildx build -t ghcr.io/janeliascicomp/colormipsearch-tools:<VERSION> . --push

Release the artifacts to Janelia Nexus Repo:

Before running the release script make sure you have an server entry for the janelia-repo in your default maven settings.xml, typically located at ~/.m2/settings.xml

<settings xmlns="http://maven.apache.org/SETTINGS/1.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd">

  <servers>
    <server>
      <id>janelia-releases</id>
      <username>yourusername</username>
      <password>yourpassword</password>
    </server>
  </servers>

</settings>

If you don't want the password in clear in settings.xml, maven offers a mechanism to encrypt it using:

mvn --encrypt-master-password <password>

to create a master password and then use

mvn --encrypt-password <password>

which you can enter in place of your password. Check maven documentation how you can do this.

To release the artifacts simply run:

./release.sh <version>

This command will also tag the repository with the <version>.

Run

Calculating the gradient score for a set of existing results

java -jar target/colormipsearch-2.8.0-jar-with-dependencies.jar \
    gradientScore \
    -rf local/testData/results/qq.json \
    -gp local/testData/flylight_40xMCFO_gradient_20px.zip \
    -rd local/testData/results.withscore

Pre-computed color depth search data

A more detailed description can be found in PrecomputedData.md.

Generate EM - LM color depth search results

The steps to generate the precomputed color depth search results are the following:

• Run createColorDepthSearchDataInput to import color depth MIPs from JACS into the Mongo database
• Run colorDepthSearch to calculate color depth matches between a mask library and a target library
• Run gradientScores to calculate gradient based score for the matches from a selected mask library
• If matching scores still need to be normalized after calculating gradient scores, run the normalizeGradientScores command
• If Patch Per Pixel matches are available, those can be imported using importPPPResults
• Run exportData command to export the results in order to be uploaded to NeuronBridge

These steps are typically handled by a set a Nextflow workflows from Precompute github repository