NIM-Studio

Plain-text, git-tracked electronic lab notebook (ELN) for reproducible bioinformatics — threads your R & Python figures into living lab notes with full provenance. Built for single-cell / CyTOF / flow cytometry; works with Obsidian, Quarto & Jupyter.

This preprocessing tool is design for 2D digital mammograms in DICOM format. It standardizes and harmonizes images through a configurable pipeline that includes spatial reorientation, pseudo-3D stacking, isotropic resampling, intensity normalization, optional denoising, contrast enhancement, and mask processing (if available).

A tool based on artificial intelligence that is able to perform a categorisation of MRI series by using standardized DICOM tags. The categorisation includes the type of sequence (e.g. spin echo, gradient echo), the weighting (e.g. T1W, T2W, DCE, ...), the presence of fat suppression and the detection of non-relevant / junk series (e.g. localizers, calibrations, screenshots...).

The tool performs a DICOM quality check in terms of correct number of files per sequence, corrupted files, precise directory hierarchy, separated dynamic series merging them, interest series filtering/selection by specific series description lists and diffusion sequence identification by b-values. It applies the desired changes to the dataset and generates a report containing information about the selected sequences, corrupted files, missing files and merged files. Status: Deployed

Thoa is a cloud bioinformatics platform. Write your Nextflow or Snakemake pipeline, point it at your data, and Thoa handles the rest: provisioning VMs (up to 12TB RAM), resolving dependencies, managing execution. No cloud expertise needed. Every job captures its full context:data, software versions, environment, machine specs, as a reproducibility artifact. Share it with a colleague and they can view or re-run the analysis without an account. Key features: AI debugger that fixes environment and dependency issues in real time. Pipeline tracking with per-step telemetry. if step 47 of 200 fails, re-run from there, not from scratch. One-click data sharing without registration. AI-assisted workflow creation from plain English. Free tier available. Starter $35/mo, Pro $109/mo, Team $480/mo. Zero-egress storage. Based in Zug, Switzerland. thoa.io​​​​​​​​​​​​​​​​