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aimseg

This project aims to accomplish the segmentation of three axonal components (axoplasm, inner cytoplasmic tongue and myelin) on TEM images using Fiji and ilastik

aimseg_dltraining

Jupyter Notebooks to train a DL pixel classifier

assess_segmentation

ImageJ macros to assess both semantic and instance segmentation.

cell_adhesion_assay

Bioimage analysis workflow for the analysis of high throughput microscpy experiments to assess cell adhesion (specifically, to quantify the binding of fluorescence-labeled cells to a cell monolayer) using Fiji

cell_detection_approaches

Bioimage analysis pipelines to detect cells (nucleus + cytoplasm) and generate label images with the aim of establishing an object hierarchy

cell_proliferation_assay

Bioimage analysis workflow for the analysis of high throughput microscopy experiments to assess cell proliferation in pulse-chase experiments (BrdU or EdU) using Fiji

dhb-venus

ImageJ macro for the detection of DHB-Venus positive cells and the quantification of its nucleus-to-cytoplasm ratio

embl-dl-course-2022

Materials for the EMBL Deep Learning course

imagej.github.io

The ImageJ wiki

label_mask_operations

neurosphere_assay

Bioimage analysis workflow for the analysis of high throughput microscpy experiments to assess neurosphere assays (or other similar assays based on spheroid growing) using Fiji and ilastik

oligodendrocyte_differentiation

other_macros

Diverse workflows to automate some simple tasks

qupath-gradle-scripting-project

region_connection_calculus

Example macros for linking 'related' objects between different binary masks, e.g., nucleus with its corresponding cytoplasm. Objects are indexed to establish their relations by means of the output matrix of the Region Connection Calculus plugin

spheroid_dl

stsm_i3s

This repository contains CellProfiler pipelines, ImageJ macros and other files generated during my NEUBIAS Short Term Scientific Mission at the scientific platforms for BioSciences Screening and Advanced Light Microscopy, Instituto de Investigação e Inovação da Universidade do Porto (Porto, Portugal)

trackmate-stardist_headless

Groovy scripts to run TrackMate-StarDist headless