Code
Open-Science Framework bacto_tracker project.HiM acquisition
python (qudi-HiM): https://github.com/NollmannLab/qudi-HiM or see published version at zenodo.
Labview: https://github.com/NollmannLab/HiMacquisitionSoft.git
See also our open-science framework Hi-M OSF project for data, archived code, and UNET networks.
HiM analysis
pyHiM: https://github.com/marcnol/pyHiM
MATLAB: http://dx.doi.org/10.17632/5f5hd9yj3z.1#folder-26d1f8c0-fc58-4b87-8c4f-cd8fa294a555
See also our open-science framework Hi-M OSF project for data, archived code, and UNET networks.
spt-PALM analysis
https://github.com/jbfiche/sptPALM.git
Code associated to Goetz, et al, Nature Communications, 2022.
https://zenodo.org/record/6811576
Code associated to Espinola, Goetz, et al, Nature Genetics, 2021.
https://github.com/NollmannLab/Espinola-Goetz-2021.git
bacto_tracker
Open-Science Framework bacto_tracker OSF project.
DCIMG to TIFF conversion
https://github.com/jbfiche/DCIMG_to_TIFF_conversion.git
MERFISH simulations
https://github.com/jbfiche/merFISH_simulation.git
Single-particle analysis
https://github.com/NollmannLab/3DreconstructionSMLM.git
Visualisation of PALM data
https://github.com/NollmannLab/vPALM2.git
python (qudi-HiM): https://github.com/NollmannLab/qudi-HiM or see published version at zenodo.
Labview: https://github.com/NollmannLab/HiMacquisitionSoft.git
See also our open-science framework Hi-M OSF project for data, archived code, and UNET networks.
HiM analysis
pyHiM: https://github.com/marcnol/pyHiM
MATLAB: http://dx.doi.org/10.17632/5f5hd9yj3z.1#folder-26d1f8c0-fc58-4b87-8c4f-cd8fa294a555
See also our open-science framework Hi-M OSF project for data, archived code, and UNET networks.
spt-PALM analysis
https://github.com/jbfiche/sptPALM.git
Code associated to Goetz, et al, Nature Communications, 2022.
https://zenodo.org/record/6811576
Code associated to Espinola, Goetz, et al, Nature Genetics, 2021.
https://github.com/NollmannLab/Espinola-Goetz-2021.git
bacto_tracker
Open-Science Framework bacto_tracker OSF project.
DCIMG to TIFF conversion
https://github.com/jbfiche/DCIMG_to_TIFF_conversion.git
MERFISH simulations
https://github.com/jbfiche/merFISH_simulation.git
Single-particle analysis
https://github.com/NollmannLab/3DreconstructionSMLM.git
Visualisation of PALM data
https://github.com/NollmannLab/vPALM2.git
Data
Rombouts, et al., Open Research Europe, 2022
Open-Science Framework bacto_tracker project.
Goetz, et al, Nature Communications, 2022.
https://zenodo.org/record/6861355
Minimal dataset to test multiplexed DNA imaging (Hi-M) software pipelines
https://zenodo.org/record/6351755
Espinola, Goetz, et al, Nature Genetics, 2021.
https://github.com/NollmannLab/Espinola-Goetz-2021.git
Cardozo et al., Molecular Cell, 2019
http://dx.doi.org/10.17632/5f5hd9yj3z.1#folder-26d1f8c0-fc58-4b87-8c4f-cd8fa294a555
Open-Science Framework bacto_tracker project.
Goetz, et al, Nature Communications, 2022.
https://zenodo.org/record/6861355
Minimal dataset to test multiplexed DNA imaging (Hi-M) software pipelines
https://zenodo.org/record/6351755
Espinola, Goetz, et al, Nature Genetics, 2021.
https://github.com/NollmannLab/Espinola-Goetz-2021.git
Cardozo et al., Molecular Cell, 2019
http://dx.doi.org/10.17632/5f5hd9yj3z.1#folder-26d1f8c0-fc58-4b87-8c4f-cd8fa294a555
Publications
Find PDFs for our publications in our Github repository here:
https://github.com/marcnol/NollmannLabPublications.git
https://github.com/marcnol/NollmannLabPublications.git