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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
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Posts
Blog Post number 1
Published:
This is a sample blog post. Lorem ipsum I can’t remember the rest of lorem ipsum and don’t have an internet connection right now. Testing testing testing this blog post. Blog posts are cool.
publications
What do we know about spatial navigation, and what else could model-based fMRI tell us?
Published in The Einstein Journal of Biology and Medicine, 2013
You can read the paper here.
Recommended citation: Tyson, A. L. (2013). "What do we know about spatial navigation, and what else could model-based fMRI tell us?" Einstein J. Biol. Med. v29 p32.
Rapid, simple and inexpensive production of custom 3D printed equipment for large-volume fluorescence microscopy
Published in International Journal of Pharmaceutics, 2015
You can read the paper heres.
Recommended citation: Tyson, A. L., Hilton, S. T., Andreae, L. C. (2015). "Rapid, simple and inexpensive production of custom 3D printed equipment for large-volume fluorescence microscopy" Int. J. Pharma. v494 p651.
Decreased functional connectivity within a language subnetwork in benign epilepsy with centrotemporal spikes
Published in Epilepsia Open, 2017
You can read the paper here.
Recommended citation: McGinnity, C. J., Smith, A. B., Yaakub, S. N., Gerbase, S. W., Gammerman, A., Tyson, A. L., Bell, T. K., Elmasri, M., Barker G. J., Richardson, M. P., Pal, D. K. (2017). "Decreased functional connectivity within a language subnetwork in benign epilepsy with centrotemporal spikes" Epilepsia Open v494 p651.
The within-subject application of diffusion tensor MRI and CLARITY reveals brain structural changes in Nrxn2 deletion mice
Published in Molecular Autism, 2019
You can read the paper here.
Recommended citation: Pervolaraki, E.*, Tyson, A. L.*, Pibiri, F., Poulter, S. L., Reichelt, A. C., Rodgers, R. J., Clapcote, S. J., Lever, C., Andreae, L. C.*, Dachtler, J.* (2019). "The within-subject application of diffusion tensor MRI and CLARITY reveals brain structural changes in Nrxn2 deletion mice" Mol. Autism v10 p8.
Optimisation and validation of hydrogel-based brain tissue clearing shows uniform expansion across anatomical regions and spatial scales
Published in Scientific Reports, 2019
You can read the paper here.
Recommended citation: Tyson, A. L., Akhtar, A., Andreae, L. C. (2019). "Optimisation and validation of hydrogel-based brain tissue clearing shows uniform expansion across anatomical regions and spatial scales" Sci. Rep. v9 #12084.
Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint
Published in Journal of Cell Biology, 2020
You can read the paper here and find the image analysis software here.
Recommended citation: Jackman, M.*, Marcozzi, C.*, Barbiero, M., Pardo, M., Yu, L., Tyson, A. L., Choudray, J., Pines, J. (2020). "Cyclin B1-Cdk1 facilitates MAD1 release from the nuclear pore to ensure a robust spindle checkpoint" J. Cell Biol. v219(6)
Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids
Published in Cell, 2020
You can read the paper here and find the software for:
- Quantification of proximity ligation assay images here.
- Quantification of acini images here.
- Quantification of calcium flux here.
Recommended citation: Koundouros, N., Karali, E., Tripp, A., Valle, A., Inglese, P., Perry, N. J. S, Magee, D. J., Virmouni, S. A., Elder, G. A., Tyson, A. L., Luisa Doria, M., van Weverwijk, A., Soares, R. F., Isacke, C. M., Nicholson, J. K., Glen, R. C., Takats, Z., Poulogiannis, G. (2020) "Metabolic Fingerprinting Links Oncogenic PIK3CA with Enhanced Arachidonic Acid-Derived Eicosanoids" Cell v181 p1
BrainGlobe Atlas API: a common interface for neuroanatomical atlases
Published in Journal of Open Source Software, 2020
You can read the paper here and find the software here.
Recommended citation: Claudi, F.*, Petrucco, L.*, Tyson, A. L.*, Branco, T., Margrie, T. W., Portugues, R. (2020) "BrainGlobe Atlas API: a common interface for neuroanatomical atlases" Journal of Open Source Software, 5(54), 2668
The retrosplenial cortex combines internal and external cues to encode head velocity during navigation
Published in bioRxiv, 2021
You can read the paper at bioRxiv.
Recommended citation: Keshavarzi, S., Bracey, E. F., Faville, R. A., Campagner, D., Tyson, A. L., Lenzi, S. C., Branco, T., Margrie, T. W. (2021). "The retrosplenial cortex combines internal and external cues to encode head velocity during navigation" bioRxiv
Analysis of segmentation ontology reveals the similarities and differences in connectivity onto L2/3 neurons in mouse V1
Published in Scientific Reports, 2021
You can read the paper here.
Recommended citation: Brown, A. P. Y.*, Cossell, L.*, Strom, M., Tyson, A. L., Vélez-Fort, M., Margrie, T.W. (2021). "Analysis of segmentation ontology reveals the similarities and differences in connectivity onto L2/3 neurons in mouse V1" Sci. Rep. v11 #4983.
Visualizing anatomically registered data with Brainrender
Published in eLife, 2021
You can read the paper at eLife or try brainrender here.
Recommended citation: Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021). "Visualizing anatomically registered data with Brainrender" eLife 2021;10:e65751
Tools for accurate post hoc determination of marker location within whole-brain microscopy images
Published in bioRxiv, 2021
You can read the paper at bioRxiv or try the software here.
Recommended citation: Tyson, A. L.*, Vélez-Fort, M.*, Rousseau, C. V., Cossell, L., Tsitoura, C., Obenhaus, H. A., Claudi, F., Lenzi, S. C., Branco, T., Margrie, T. W. (2021). "Tools for accurate post hoc determination of marker location within whole-brain microscopy images" bioRxiv
A deep learning algorithm for 3D cell detection in whole mouse brain image datasets
Published in PLoS Computational Biology, 2021
You can read the paper at PLoS Computational Biology or try the software here.
Recommended citation: Tyson, A. L.*, Rousseau, C. V.*, Niedworok, C. J.*, Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., Margrie, T. W. (2021). "A deep learning algorithm for 3D cell detection in whole mouse brain image datasets" PLoS Comp Bio 17(5): e1009074.
Mesoscale microscopy and image analysis tools for understanding the brain
Published in Progress in Biophysics and Molecular Biology, 2021
You can read the paper here.
Recommended citation: Tyson, A. L., Margrie, T. W. (2021). "Mesoscale microscopy and image analysis tools for understanding the brain" Progress in Biophysics and Molecular Biology
software
CalciumAnalysis - analysis of calcium dynamics in 2D images.
MATLAB software as used for the quantification of calcium flux in Koundouros et al. (2020). Segments cells in 2D images and extracts the timecource of cellular calcium fluoresence. See the GitHub repo here.
cell-coloc3D - measure distribution of a marker per cell in a manually segmented object
MATLAB software as used for the quantification of 3D acini formation in Koundouros et al. (2020). Following manual segmentation of a structure (e.g. a spheroid), individual cells are segmented, and the expression of a marker within these cells is quantified. See the GitHub repo here.
coloc3DT - measuring colocalisation of 3D functional images
Python software for measuring the colocalisation of N channels in another, segmented channel, as used in Jackman & Marcozzi et al. (2020). See the GitHub repo here.
foci2D - measure foci per cell in 2D images
MATLAB software as used for the analysis of the proximity ligation assay in Koundouros et al. (2020). Counts the number of foci per cell in 2D, based on a segmented nuclear marker. See the GitHub repo here.
fancylog - fancier logging in Python.
See the GitHub repo here.
micrometa - parsing of whole-brain microscopy metadata.
See the GitHub repo here.
slurmio - a lightweight Python package to interface with the slurm workload manager.
See the GitHub repo here.
BrainGlobe
Along with Federico Claudi and Luigi Petrucco, we have developed: BrainGlobe: Open python tools for morphological analyses in systems neuroscience.
Whole-brain microscopy image analysis
I’m developing tools for the analysis and visualisation of whole-brain microscopy images. This includes:
- cellfinder for 3D cell detection (paper)
- brainreg for 3D registration and atlas-based segmentation
- brainreg-segment for segmentation and analysis of bulk structures (e.g. Neuropixels probes, injection sites)
talks
teaching
Introduction to Image Analysis in FIJI
Technical course, Institute of Cancer Research, 2018
Introduction to fundamental image analysis using FIJI for students & staff, taught at the Institute of Cancer Research, London, U.K. Slides and course materials can be found here.
PyStarters - Introduction to Python Programming
Technical course, Sainsbury Wellcome Centre, 2018
Ongoing Python programming and general software carpentry course (with a focus on neuroscience) taught at the Sainsbury Wellcome Centre, UCL, U.K. All materials can be found here.