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mAIcrobe validation datasets
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
File Size1004.7 MB
Data TypeDataset
Published2026
Licensecc-by-4.0
Total Views278
Total Downloads332
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
- COL_WT_Timelapse
- Widefield 2D+t timelapse of Staphylococcus aureus COL WT (membrane + phase contrast)
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: D
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Files are hosted on the source repository. Click download to access the full dataset.
Brito, António (2026). mAIcrobe validation datasets. https://doi.org/10.5281/zenodo.21062578