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https://github.com/jboulanger/fish-octopus

https://github.com/jboulanger/fish-octopus

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
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    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (8.4%) to scientific vocabulary
Last synced: 5 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: jboulanger
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 4.43 MB
Statistics
  • Stars: 0
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Created about 2 years ago · Last pushed 8 months ago
Metadata Files
Readme

README.md

RNA expression levels in the brains of paralarval Octopus vulgaris

DOI

Image analysis pipeline to quantify and spatially localise RNA expression levels in the brains of paralarval Octopus vulgaris, using in situ hybridisation chain reaction (HCR).

Nuclei are segmented using cellpose with the 'nuclei' pretrained model and the fish signal is quantified using a difference of Gaussian filter.

Workflow on a workstation:

  1. 1Scanfolder.ipynb to create a list of files to work with
  2. 2SelectROI.ipynb to define regions of interest
  3. 3_Process.ipynb to process all files
  4. 4_Visualization.ipynb to visualize the results and compute statistics.

Remote processing:

Configuration

  • In a terminal connect to the login node, eg: bash ssh hex
  • get the code on the system, eg: bash mkdir code cd code git clone https://github.com/jboulanger/fish-octopus.git ### Processing files
  • connect to hex via visual code to edit the file script.sh
  • run bash sbatch --array 10 script.sh replacing 10 by the number of lines in the filelist.csv.

Files organization

  • source folder

    • img1.ims
    • img2.ims
    • img3.ims

  • destination

    • filelist.csv (after step 1)
    • img1-regions.json (after step 2)
    • img1-labels.tif (after step 3)
    • img1-measurements.csv (after step 3)
    • img1-stats.csv (after step 4)
    • ... (for files img2.ims, img3.ims)

Installation

To create an environment from scratch: ```bash

install micromamba

"${SHELL}" <(curl -L micro.mamba.pm/install.sh)

reload the shell

${SHELL}

Clone the repository

git clone https://github.com/jboulanger/fish-octopus cd fish-octopus

create an environment

micromamba -qy create -f environment.yml

activate the environment

micromamba activate acourtney-fish-octopus ```

Owner

  • Login: jboulanger
  • Kind: user

GitHub Events

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  • Release event: 1
  • Public event: 1
  • Push event: 3
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Last Year
  • Release event: 1
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  • Push event: 3
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