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