Repositories list

• prepareImagesMACSima

  Public
  This groovy script extracts, renames and merges the images corresponding to the MACSima capture cycles. Specifically, for each ROI it renames the images of the different channels with the name of the corresponding marker and joins them into a single merged TIFF image.

  Groovy

  •0•0•0•0•Updated May 26, 2025May 26, 2025

• telomere_quantification

  Public
  Python

  •0•0•0•0•Updated May 8, 2025May 8, 2025

• 3DmicrogliaAnalysis_code

  Public
  This repository contains scripts for image analysis using Groovy and Python. The scripts are designed to process and analyze confocal microscopy images, specifically focusing on cell segmentation and marker quantification.

  Groovy

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Apr 11, 2025Apr 11, 2025

• QuPath_course_CMU_CNIO

  Public
  This is a repository with the guide and datasets created for a QuPath course in the Confocal Microscopy Unit at CNIO

  GNU General Public License v3.0

  •0•0•0•0•Updated Apr 11, 2025Apr 11, 2025

• 3DWholeSpotAnalysis_

  Public
  This repository contains a Nextflow pipeline for processing and analyzing microscopy images. The pipeline includes steps for converting LIF files to TIFF, segmenting images using Cellpose, merging images, and performing telomere analysis.

  Groovy

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Apr 7, 2025Apr 7, 2025

• .github

  Public
  The CMU supports with advanced bioimage analysis to extract meaningful quantitative information from microscopy datasets.

  0•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• 3DOrganoidAnalysis_

  Public
  This repository contains a robust methodology for identifying and characterizing organoids using the Cellpose1 algorithm. The script allows for precise 3D identification of individual organoids based on the overlay of GFP and Tomato markers.

  Groovy

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 18, 2024Sep 18, 2024

• 2DColocGfpKi67_code

  Public
  This groovy script helps to quantify 2D Colocalization GFP/ki67+

  Groovy

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Sep 14, 2023Sep 14, 2023

• cellDistanceClassification

  Public
  This groovy script helps to quantify min distances among cells to classify them into single, nearby attached and umbrella cells.

  Groovy

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• doublePositiveQuantification

  Public
  This Groovy script helps to quantify single positive and double positive nuclei in fluorescence multi-channel image

  Groovy

  •0•0•0•0•Updated Aug 17, 2023Aug 17, 2023

• fluorescenceQuantification_code

  Public
  This Groovy script helps to quantify fluorescence intensity statistics in Nuclei and cytoplasm

  Groovy

  •0•0•0•0•Updated Aug 9, 2023Aug 9, 2023

• embryoMorphoIntensity_

  Public
  This is a python/groovy workflow to evaluate 3D morphology and intensity on early embryo and late blastocyst

  Groovy

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 7, 2023Aug 7, 2023

• cellQuantification_code

  Public
  This groovy script helps to quantify positive areas of overlapping among cells

  Groovy

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 12, 2023Jul 12, 2023

• QuPath_Cellpose_StarDist_Extension

  Public
  This is a repo to store Groovy scripts to run CellPose and StarDist functionalities within QuPath enviroment

  Groovy

  •1•1•0•0•Updated Jun 22, 2023Jun 22, 2023

• tissueVascularizationMeasure

  Public
  This is a Groovy script to work within QuPath environment to identify vascular areas and measure on different channels

  Groovy

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jun 21, 2023Jun 21, 2023