DOI: 10.5281/zenodo.17306840
title: mAIcrobe validation datasets

description: mAIcrobe dataset collection — Overview

This repository aggregates several bacterial microscopy datasets used for cell-cycle analysis, morphometrics, and deep-learning segmentation. Used in mAIcrobe

https://maicrobe.henriqueslab.org

https://github.com/HenriquesLab/mAIcrobe

 

Folder map

All folder contain a README.md with details on the dataset, acquisition, and references.



JE2_WT



 SIM images of Staphylococcus aureus JE2 WT (membrane + DNA channels)



LCML1_LCML262



SIM images of CRISPRi dnaA knockdown (LCML1) and control (LCML262)



StarDist_Saureus



Training and test data for StarDist segmentation on S. aureus SIM images



 UNetSPneumo



 Training and test data for U-Net segmentation on Streptococcus pneumoniae phase-contrast images




JE2_WT 



31 fields of view (FOVs) of S. aureus JE2 WT imaged by structured illumination microscopy (SIM).

Channels: membrane (NileRed) and DNA (Hoechst 33342).

Dataset used to validate eHooke’s cell-cycle model; repurposed to validate morphometrics in mAIcrobe.

Reference: Saraiva BM, Krippahl L, Filipe SR, Henriques R, Pinho MG. Biological Imaging. 2021;1:e3. doi:10.1017/S2633903X21000027.


 

LCML1_LCML262



Scope: Two S. aureus datasets, membrane-labelled and imaged by SIM.

LCML1: CRISPRi-mediated knockdown of dnaA.

LCML262: Control strain with dCas9 and markers but no sgRNA.

Each dataset contains 5 FOVs.

Reference (strain resource): Reed P et al. 2024. mBio 15:e02773-23. https://doi.org/10.1128/mbio.02773-23


StarDist_Saureus



Goal: Data for training/testing StarDist instance segmentation on S. aureus SIM membrane images (used in mAIcrobe).

Training set:



Conditions: WT JE2 (10 FOVs) and WT JE2 + PC190723 (12 FOVs; FtsZ inhibitor causing enlarged bacteria).

Contents: Fluorescence images + corresponding instance masks (Labels match image filenames per subset).



Test set:



Condition: LCML262 (3 FOVs).

Contents: Images + instance masks.



References:



Ferreira MG et al. (ReScale4DL) bioRxiv, 2025. https://doi.org/10.1101/2025.04.09.647871

Reed P et al. mBio, 2024. https://doi.org/10.1128/mbio.02773-23




UNetSPneumo



Goal: Data for training/testing a U‑Net model on phase-contrast images of Streptococcus pneumoniae (Pen6; PenR, unencapsulated; mosaic pbp alleles). Trained with ZeroCostDL4Mic.

Size (from README):



16 FOVs for training

3 FOVs for testing



Structure (with filename parity between images and masks):



Train/Phase

Train/Labels

Test/Phase

Test/Labels




Citations



Saraiva BM, Krippahl L, Filipe SR, Henriques R, Pinho MG. eHooke: Automated image analysis of spherical bacteria. Biological Imaging. 2021;1:e3. doi:10.1017/S2633903X21000027

Reed P, Sorg M, Alwardt D, Serra L, Veiga H, Schäper S, Pinho MG. 2024. A CRISPRi-based genetic resource to study essential Staphylococcus aureus genes. mBio 15:e02773-23. https://doi.org/10.1128/mbio.02773-23

Ferreira MG, Saraiva BM, Brito AD, Pinho MG, Henriques R, Gómez-de-Mariscal E. ReScale4DL: Balancing Pixel and Contextual Information for Enhanced Bioimage Segmentation. bioRxiv, 2025. https://doi.org/10.1101/2025.04.09.647871