Repositories list

• cylinder-time-lapse

  Public
  Jupyter Notebook

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  BSD 3-Clause "New" or "Revised" License

  •0•0•0•1•Updated Feb 27, 2025Feb 27, 2025

• cylinder-penetration

  Public
  Python

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  MIT License

  •0•0•0•0•Updated Feb 25, 2025Feb 25, 2025

• Ariadne

  Public
  Python

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  GNU General Public License v3.0

  •1•2•4•1•Updated Jan 14, 2025Jan 14, 2025

• PAT-Pipeline-for-Analysis-of-Periderm

  Public
  Python

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  MIT License

  •2•0•0•1•Updated Jan 24, 2024Jan 24, 2024

• camera_calibration

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Nov 21, 2023Nov 21, 2023

• aws-s3-desktop-uploader

  Public
  Python script for uploading files to an AWS S3 bucket with some additional features

  Python

  •0•0•1•0•Updated Jun 3, 2023Jun 3, 2023

• data-system

  Public
  The main Salk HPI Data System for tracking plants and their phenotypic data in the lab, greenhouse, and field. Integrates with QR code tracking. Makes querying past experiments (+ images, etc.) and environmental data easier.

  Python

  •0•0•2•2•Updated Jan 28, 2023Jan 28, 2023

• plant-independent-image-uploader

  Public
  Uploading standalone images to AWS

  Python

  •0•0•0•0•Updated Jan 26, 2022Jan 26, 2022

• chorylab-HyDE

  Public
  This is the official repo for HyDE (Hypocotyl Determining Engine), a hardware and software pipeline that measures hypocotyl growth in time-series images. By Benjamin J. Cole

  MATLAB

  •0•0•0•0•Updated Jan 2, 2022Jan 2, 2022

• greenhouse-giraffe-uploader

  Public
  Python-based Windows service to upload Giraffe images to AWS S3. The Giraffe is a custom imaging apparatus we use in our greenhouse.

  Python

  •0•0•0•0•Updated Mar 26, 2021Mar 26, 2021

• plant-cylinder-uploader

  Public
  Python-based Windows service to upload cylinder images to AWS S3

  Python

  •0•1•0•0•Updated Mar 26, 2021Mar 26, 2021

• DSLR-camera-barcode-imaging-guide

  Public
  Control a Sony A7RII camera (normal DSLR camera) from a Windows computer and integrate with barcode scanning to image some artifacts at high throughput. This guide will allow you to set the filename of each image as the value scanned from the label.

  0•0•0•0•Updated Mar 24, 2021Mar 24, 2021

• nsipptparser

  Public
  Very simple Python package to parse .nsippt files to json

  Python

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  MIT License

  •0•0•0•0•Updated Mar 22, 2021Mar 22, 2021

• greenhouse-giraffe-uploader-ABANDONED

  Public
  Repo ABANDONED in favor of https://github.com/Salk-Harnessing-Plants-Initiative/greenhouse-giraffe-uploader

  Python

  •0•0•0•0•Updated Feb 2, 2021Feb 2, 2021

• buschlab-BratV2-Analysis

  Public
  BRAT V2 Analysis, a plugin that is ostensibly equivalent to the BRAT V2 plugin (plugin 1 of the BRAT pipeline) except skips the segmentation part and only does the analysis part. This is is intended to co-opt the BRAT pipeline with the new DeepBRAT project.

  Java

  •0•0•0•0•Updated Jan 21, 2021Jan 21, 2021

• excel-barcode-scanner-guide

  Public
  Excel technique that allows you to quickly scan a barcode (or QR code) to find a row and input a value associated with that row

  1•0•0•0•Updated Jan 18, 2021Jan 18, 2021

• buschlab-BratV2-Analysis-Binaries

  Public
  These are the binaries for BRAT V2 Analysis, a plugin that is ostensibly equivalent to the BRAT V2 plugin (plugin 1 of the BRAT pipeline) except skips the segmentation part and only does the analysis part. This is is intended to co-opt the BRAT pipeline with the new DeepBRAT project.

  0•0•0•0•Updated Jan 11, 2021Jan 11, 2021

• buschlab-BratV2-Lotus-Binaries

  Public
  Official compiled binaries of BRAT V2 for use with Lotus

  0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-TifMaskWriter

  Public
  Create tif files from brat output for machine learning input

  Java

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-rootscope-MMPlugin

  Public
  This is the main plugin for MicroManager 1.4

  Java

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-rootscope-gRPC-Server

  Public
  This is the server implementation for the Rootscope project

  Java

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-rootscope-gRPC-Client

  Public
  This is the JavaFx client for the Rootscope project

  Java

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-R_RNAseq_scripts

  Public
  Collection of various R snippets for RNA diffseq analyses

  R

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-MultiScan

  Public
  Official repo for Busch Lab MultiScan (plant plate scanner) software

  Java

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-BratV2-Arabidopsis-Binaries

  Public
  Official compiled binaries of BRAT V2 for use with Arabidopsis

  0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-Multi-Scan-Binaries

  Public
  Compiled binaries for Busch Lab MultiScan (plant plate scanner) software

  0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-mtl

  Public
  Multi trait limix

  Python

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-GeneHunter

  Public
  This is a small program to create and query a SQLITE database containing data from the TAIR project.

  Python

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  Other

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-lightsheet-autofocus-detection

  Public
  Python program for focus detection for the lightsheet microscope project. Takes image stacks and analyses the "best" focus based on Normalized Variance (Groen et al., 1985; Yeo et al., 1993) and AutoCorrelation (Vollath, 1987, 1988)

  Python

  •0•0•0•0•Updated Jan 4, 2021Jan 4, 2021

• buschlab-Confocal-Tracking

  Public
  0•0•0•0•Updated Jan 4, 2021Jan 4, 2021