Awesome

Imaging analysis tools

A table containing imaging analysis tools for biology and neuroscience, with a focus on calcium imaging.

Created by <a href='https://bahanonu.com' target='_blank'>Biafra Ahanonu, PhD</a> (<a href='https://www.hhmi.org/scientists/biafra-ahanonu' target='_blank'>HHMI Hanna Gray Fellow</a>, <a href='https://basbaumlab.ucsf.edu/people/' target='_blank'>Basbaum Lab</a>, UCSF).

The table can also be found at:

• https://bahanonu.com/brain/imaging_tools/
• https://bahanonu.com/syscarut/articles/233/
• If you would like to cite this table, see Cite this repository in the right About section or https://zenodo.org/record/8349533.

Notes:

• I use cell extraction to refer to algorithms that perform cell segmentation and extract neural activity traces.
• In cases where the publication did not explicitly give the algorithm a name, made one based on the underlying method used.
• This table includes algorithms that simultaneously extract cell images/contours and reconstruct cell activity traces along with ones mainly focused on determining one or the other.
• Several calcium imaging related packages have also been included along with algorithms dealing with post-hoc handling of data or cell activity traces.
• Future versions of the repository will include table file (e.g. CSV) and basic LaTeX code so others can import or modify the table more easily going forward.
• Depending on monitor size and browser, scroll horizontally to see right-most table columns (e.g. websites/URLs).
• Any additional papers or algorithms that should be added or suggested updates to the table, leave a <a href='https://bahanonu.com/syscarut/articles/226/' target='_blank'>comment on the associated blog post</a> or open an issue on the GitHub page, I want to make sure everyone’s brilliant work is acknowledged!

Josien PW Pluim. Elastix: a toolbox for intensity-based medical image registration. <span class="rm-lmri-12">IEEE transactions on medical imaging</span>, 29(1):196–205, 2009.

Automated identification of neuronal activity from calcium imaging by sparse dictionary learning. In <span class="rm-lmri-12">Biomedical Imaging (ISBI), 2013 IEEE 10th</span> <span class="rm-lmri-12">International Symposium on</span>, pages 1058–1061. IEEE, 2013.

Peyrache. Neurodata without borders: creating a common data format for neurophysiology. <span class="rm-lmri-12">Neuron</span>, 88(4):629–634, 2015.

et al. Netcal: An interactive platform for large-scale, network and population dynamics analysis of calcium imaging recordings, zenodo (2017).

Samuroi, a python-based software tool for visualization and analysis of dynamic time series imaging at multiple spatial scales. <span class="rm-lmri-12">Frontiers in</span> <span class="rm-lmri-12">neuroinformatics</span>, 11:44, 2017.

Miniscope 1-Photon-Based Calcium Imaging Signal Extraction Pipeline. <span class="rm-lmri-12">Cell Reports</span>, 23(12):3673–3684, 2018. ISSN 2211-1247.

Paul W Frankland, and Sheena A Josselyn. Automated curation of cnmf-e-extracted roi spatial footprints and calcium traces using open-source automl tools. <span class="rm-lmri-12">bioRxiv</span>, 2020a.

learning, instance segmentation, and correlations for cell segmentation in calcium imaging. In <span class="rm-lmri-12">Medical Image Computing and Computer Assisted</span> <span class="rm-lmri-12">Intervention–MICCAI 2020: 23rd International Conference, Lima, Peru,</span> <span class="rm-lmri-12">October 4–8, 2020, Proceedings, Part V 23</span>, pages 151–162. Springer, 2020.

Chris van der Togt. Specseg: cross spectral power-based segmentation of neurons and neurites in chronic calcium imaging datasets. <span class="rm-lmri-12">bioRxiv</span>, pages 2020–10, 2021.

imaging and synchronized neuron firing detection. In <span class="rm-lmri-12">2021 43rd Annual</span> <span class="rm-lmri-12">International Conference of the IEEE Engineering in Medicine & Biology</span> <span class="rm-lmri-12">Society (EMBC)</span>, pages 2997–3003. IEEE, 2021.

is a versatile toolbox that segments neurons and neurites in chronic calcium imaging datasets based on low-frequency cross-spectral power. <span class="rm-lmri-12">Cell reports</span> <span class="rm-lmri-12">methods</span>, 2(10), 2022.

and correction for simultaneous multi-plane two-photon calcium imaging. <span class="rm-lmri-12">Biomedical Optics Express</span>, 13(4):2035–2049, 2022.

Sakaguchi. The caliali tool for long-term tracking of neuronal population dynamics in calcium imaging. <span class="rm-lmri-12">bioRxiv</span>, pages 2023–05, 2023.