Tracking cell lineages in 3D by incremental deep learning

Deep learning is emerging as a powerful approach for bioimage analysis. Its use in cell tracking is limited by the scarcity of annotated data for the training of deep-learning models. Moreover, annotation, training, prediction, and proofreading currently lack a unified user interface. We present ELEPHANT, an interactive platform for 3D cell tracking that addresses these challenges by taking an incremental approach to deep learning. ELEPHANT provides an interface that seamlessly integrates cell track annotation, deep learning, prediction, and proofreading. This enables users to implement cycles of incremental learning starting from a few annotated nuclei. Successive prediction-validation cycles enrich the training data, leading to rapid improvements in tracking performance. We test the software’s performance against state-of-the-art methods and track lineages spanning the entire course of leg regeneration in a crustacean over 1 week (504 timepoints). ELEPHANT yields accurate, fully-validated cell lineages with a modest investment in time and effort.

The Critical Importance of Spatial and Temporal Scales in Designing and Interpreting Immune Cell Migration Assays

Intravital microscopy and other direct-imaging techniques have allowed for a characterisation of leukocyte migration that has revolutionised the field of immunology, resulting in an unprecedented understanding of the mechanisms of immune response and adaptive immunity. However, there is an assumption within the field that modern imaging techniques permit imaging parameters where the resulting cell track accurately captures a cell’s motion. This notion is almost entirely untested, and the relationship between what could be observed at a given scale and the underlying cell behaviour is undefined. Insufficient spatial and temporal resolutions within migration assays can result in misrepresentation of important physiologic processes or cause subtle changes in critical cell behaviour to be missed. In this review, we contextualise how scale can affect the perceived migratory behaviour of cells, summarise the limited approaches to mitigate this effect, and establish the need for a widely implemented framework to account for scale and correct observations of cell motion. We then extend the concept of scale to new approaches that seek to bridge the current “black box” between single-cell behaviour and systemic response.

Feminist Science Interventions in Self-Tracking Technology

Contemporary self-tracking systems signal a new era of biological monitoring now entangled with the politics of ubiquitous computing. Is self-tracking technology, which is connected to major stakeholders in healthcare, essential for filling in gaps in care, or is it fueling an increasingly commercialized medical industry? This essay examines the complex biases embedded in self-tracking technologies and introduces three manifestations of feminist science that subvert the monetization of personal health information: feminist art collective subRosa, which investigates how personal genetic information is developed into marketable medical products in their web-based project, Cell Track: Mapping the Appropriation of Life Materials; media artist and biohacker Mary Maggic, who makes self-synthesized hormone therapy accessible with their Open Source Estrogen project; artist-researcher Heather Dewey-Hagborg, whose biohacking products provide a DIY science in a world marred by genetic policing. Against the lure of connectivity, feminist science looks to circumvention as a method for understanding and disrupting the gendered and raced politics embedded in self-tracking technology. Tracing alternative techno-politics in these three new media projects, this essay reveals the necessity for artistic interventions in the contemporary healthcare landscape. Feminist art collective subRosa investigates how personal genetic information is developed into marketable medical products in their web-based project, Cell Track: Mapping the Appropriation of Life Materials. Drawing attention to the corporate ownership of biology, Cell Track adds new meaning to the idea of tracking. Similarly emphasizing the potential in citizen science, media artist and biohacker Mary Maggic makes self-synthesized hormone therapy accessible with their Open-Source Estrogen project. Both subRosa and Maggic are interested in bypassing institutional gatekeepers, not unlike artist-researcher Heather Dewey-Hagborg whose biohacking products suggest a DIY science in a world marred by genetic policing. Feminist science aims to circumvent tracking and institutional biopower against targeted populations. Against the lure of connectivity, feminist science looks to circumvention as a method for understanding and disrupting the gendered and raced politics embedded in surveillance. Working through the three bioart projects above, this essay reveals the necessity for artistic interventions in the contemporary healthcare landscape. Where commercial self-tracking products shortchange consumers by requiring them to share their health data with third-party companies, a feminist science framework and practice critically examines – and in some cases offers a departure from – the neoliberal biotechnology and medical industries.

Photoreceptor for Curling Behavior in Peranema trichophorum and Evolution of Eukaryotic Rhodopsins

ABSTRACT When it is gliding, the unicellular euglenoid Peranema trichophorum uses activation of the photoreceptor rhodopsin to control the probability of its curling behavior. From the curled state, the cell takes off in a new direction. In a similar manner, archaea such as Halobacterium use light activation of bacterio- and sensory rhodopsins to control the probability of reversal of the rotation direction of flagella. Each reversal causes the cell to change its direction. In neither case does the cell track light, as known for the rhodopsin-dependent eukaryotic phototaxis of fungi, green algae, cryptomonads, dinoflagellates, and animal larvae. Rhodopsin was identified in Peranema by its native action spectrum (peak at 2.43 eV or 510 nm) and by the shifted spectrum (peak at 3.73 eV or 332 nm) upon replacement of the native chromophore with the retinal analog n-hexenal. The in vivo physiological activity of n-hexenal incorporated to become a chromophore also demonstrates that charge redistribution of a short asymmetric chromophore is sufficient for receptor activation and that the following isomerization step is probably not required when the rest of the native chromophore is missing. This property seems universal among the Euglenozoa, Plant, and Fungus kingdom rhodopsins. The rhodopsins of animals have yet to be studied in this respect. The photoresponse appears to be mediated by Ca2+ influx.

Rapid, microtubule-dependent fluctuations of the cell margin

Using data automatically acquired by microinterferometry from large numbers of chick fibroblasts, we have detected rapid microfluctuations in the rates of protrusion and retraction of the cell margin which were strongly suppressed by colcemid, nocodazole and taxol. Fluctuations in the rate of retraction of the margin were about twice as powerful as fluctuations in the rate of protrusion. High-frequency fluctuations were also apparent in the cell track and in measures of cell spreading, shape and speed. These rapid fluctuations were also all suppressed by colcemid and nocodazole, sometimes by doses insufficient to disrupt the majority of microtubules. Taxol on the other hand did not suppress fluctuations in direction of the cell track nor fluctuations in the spreading of the cells but it was very effective at suppressing variations in protrusion and retraction and in cell speed and shape. We discovered that much slower, larger-scale variations in protrusion, retraction, spreading, shape and speed resulted from the accumulation of these rapid, microtubule-dependent fluctuations of the cell margin. These large-scale variations in cell behaviour were also suppressed by the same drug treatments that were effective in suppressing the corresponding high-frequency fluctuations. We speculate that a function of microtubules is to enhance the fibroblast's responses to its environment by causing microfluctuations of the cell's margin which give rise to large-scale variations in cell behaviour.