Explore projects

Stand to hold a sample chamber of a Zeiss lightheet horizontally during preparation

A brief illustration of how Marimo can be useful for image analysis pipelines and user-ready deliverable applications. Originally presented at BioOptics meeting 2024

FPulse is data acquistion system for patch-clamp recordings, based in CED1401 hardware, and IgorPro.

Simple Jupyter based user interface to [CARE] (http://csbdeep.bioimagecomputing.com/) and Noise2void

This program allows a series of tests over illumination sources for Zeiss widefield and confocal microscopes running Zen Blue. It is possibe to test:

Short term stability: According to QUAREP-LiMi full test is completed in 5 minutes for each illumination line, testing powers every second. Long term stability: The QUAREP-LiMi protocol stablishes 2h tests per line, with measurement intervals of 30s. To allow this for multiple lines this program interleaves the tests for all lines every interval, allowing the full check to be completed in a single run. Linearity (response): To analyze the linearity -or response curve- of each light source the powers are measured for a series of set powers. These tests can be performed for the desired lines and for different test conditions.

A more general (arb. pixel format, fractional shift, stacks) reimplementation of https://imagej.net/ij/plugins/correct-shift.html to perform post-acquisition bi-directional scanning correction.

Code related to research on MRF MAP inference.

Code for Hybrid Method

Workshop about FAIR principles, research data management (RDM) and good practices in figure generation by the Imaging and Optics Facility (IOF) team at ISTA.