A fast, fully automated cell segmentation algorithm for high-throughput and high-content screening

High-throughput, high-content screening (HT-HCS) of large compound libraries for drug discovery imposes new constraints on image analysis algorithms. Time and robustness are paramount while accuracy is intrinsically statistical. In this article, a fast and fully automated algorithm for cell segmentation is proposed. The algorithm is based on a strong attachment to the data that provide robustness and have been validated on the HT-HCS of large compound libraries and different biological assays. We present the algorithm and its performance, a description of its advantages and limitations, and a discussion of its range of application.

Three-dimensional point spread function model for line-scanning confocal microscope with high-aperture objective

Point Spread Function (PSF) modelling is an important task in image formation analysis. In confocal microscopy, the exact PSF is rarely known, thus one has to rely on its approximation. An initial estimation is usually performed experimentally by measuring fluorescent beads or analytically by studying properties of the optical system. Yet, fluorescent line-scanning confocal microscopes are not widespread; therefore, very few adapted models are available in the literature. In this paper, we propose an analytical PSF model for line-scanning confocal microscopes. Validation is performed by measuring the error between our model and an experimental PSF measured with fluorescent beads, assumed to represent the real PSF. Comparison with existing models is also presented.

Bias image correction via stationarity maximization

Automated acquisitions in microscopy may come along with strong illumination artifacts due to poor physical imaging conditions. Such artifacts obviously have direct consequences on the efficiency of an image analysis algorithm and on the quantitative measures. In this paper, we propose a method to correct illumination artifacts on biological images. This correction is based on orthogonal polynomial modeling, combined with stationary maximization criteria. To validate the proposed method we show that we improve particle detection algorithm.

Callosal connections of dorso-lateral premotor cortex

This study investigated the organization of the callosal connections of the two subdivisions of the monkey dorsal premotor cortex (PMd), dorso-rostral (F7) and dorso-caudal (F2). In one animal, Fast blue and Diamidino yellow were injected in F7 and F2, respectively; in a second animal, the pattern of injections was reversed. F7 and F2 receive a major callosal input from their homotopic counterpart. The heterotopic connections of F7 originate mainly from F2, with smaller contingent from pre-supplementary motor area (pre-SMA, F6), area 8 (frontal eye fields), and prefrontal cortex (area 46), while those of F2 originate from F7, with smaller contributions from ventral premotor areas (F5, F4), SMA-proper (F3), and primary motor cortex (M1). Callosal cells projecting homotopically are mostly located in layers II-III, those projecting heterotopically occupy layers II-III and V-VI. A spectral analysis was used to characterize the spatial fluctuations of the distribution of callosal neurons, in both F7 and F2, as well as in adjacent cortical areas. The results revealed two main periodic components. The first, in the domain of the low spatial frequencies, corresponds to periodicities of cell density with peak-to-peak distances of approximately 10 mm, and suggests an arrangement of callosal cells in the form of 5-mm wide bands. The second corresponds to periodicities of approximately 2 mm, and probably reflects a 1-mm columnar-like arrangement. Coherency and phase analyses showed that, although similar in their spatial arrangements, callosal cells projecting to dorsal premotor areas are segregated in the tangential cortical domain.

Eye-Hand Coordination during Reaching. I. Anatomical Relationships between Parietal and Frontal Cortex

The anatomical and physiological substrata of eye-hand coordination during reaching were studied through combined anatomical and physiological techniques. The association connections of parietal areas V6A and PEc, and those of dorso-rostral (F7) and dorso-caudal (F2) premotor cortex were studied in monkeys, after physiological characterization of the parietal regions where retrograde tracers were injected. The results show that parieto-occipital area V6A is reciprocally connected with F7, and receives a smaller projection from F2. Local parietal projections to V6A arise from areas MIP and, to a lesser extent, 7m, PEa and PEC: On the contrary, parietal area PEc is strongly and reciprocally connected with the part of F2 located close to the pre-central dimple (pre-CD). Local parietal projections to PEc come from a distributed network, including PEa, MIP, PEci and, to a lesser extent, 7m, V6A, 7a and MST. Premotor area F7 receives parietal projections mainly from 7m and V6A, and local frontal projections mainly from F2. On the contrary, premotor area F2 in the pre-CD zone receives parietal inputs from PEc and, to a lesser extent, PEci, while in the peri-arcuate zone F2 receives parietal projections from PEa and MIP. Local frontal projections to F2 pre-CD mostly stem from F4, and, to a lesser extent, from F7 and F3, and CMAd; those addressed to peri-arcuate zone of F2 arise mainly from F5 and, to a lesser extent, from F7, F4, dorsal (CMAd) and ventral (CMAv) cingulate motor areas, pre-supplementary (F6) and supplementary (F3) motor areas. The distribution of association cells in both frontal and parietal cortex was characterized through a spectral analysis that revealed an arrangement of these cells in the form of bands, composed of cell clusters, or 'columns'. The reciprocal connections linking parietal and frontal cortex might explain the presence of visually related and eye-position signals in premotor cortex, as well as the influence of information about arm position and movement direction in V6A and PEC: The association connections identified in this study might carry sensory as well motor information that presumably provides a basis for a re-entrant signaling. This might be necessary to match retinal-, eye- and hand-related information underlying eye-hand coordination during reaching.

Eye-Hand Coordination during Reaching. II. An Analysis of the Relationships between Visuomanual Signals in Parietal Cortex and Parieto-frontal Association Projections

The relationships between the distribution of visuomanual signals in parietal cortex and that of parieto-frontal projections are the subject of the present study. Single cell recording was performed in areas PEc and V6A, where different anatomical tracers were also injected. The monkeys performed a variety of behavioral tasks, aimed at studying the visual and motor properties of parietal cells, as well as the potential combination of retinal-, eye- and hand-related signals on cell activity. The activity of most cells was related to the direction of movement and the active position of the hand. Many of these reach-related cells were influenced by eye position information. Fewer cells displayed relationships to saccadic eye movements. The activity of most neurons related to a combination of both hand and eye signals. Many cells were also modulated during preparation for hand movement. Light-dark differences of activity were common and interpreted as related to the sight and monitoring of hand motion and/or position in the visual field. Most cells studied were very sensitive to moving visual stimuli and also responded to optic flow stimulation. Visual receptive fields were generally large and extended to the periphery of the visual field. For most neurons, the orientation of the preferred directions computed across different epochs and tasks conditions clustered within a limited sector of space, the field of global tuning. This can be regarded as an ideal frame to combine spatially congruent eye- and hand-related information for different forms of visuomanual behavior. All these properties were common to both PEc and V6A. Retinal, eye- and hand-related activity types, as well as parieto-frontal association cells, were distributed in a periodic fashion across the tangential domain of areas PEc and V6A. These functional and anatomical distributions were characterized and compared through a spectral and coherency analysis, which revealed the existence of a selective 'match' between activity types and parieto-frontal connections. This match depended on where each individual efferent projection was addressed. The results of the present and of the companion study can be relevant for a re-interpretation of optic ataxia as the consequence of the breakdown of the combination of retinal-, eye- and hand-related directional signals within the global tuning fields of parietal neurons.

Early coding of visuomanual coordination during reaching in parietal area PEc

The parietal mechanisms of eye-hand coordination during reaching were studied by recording neural activity in area PEc while monkeys performed different tasks, aimed at assessing the influence of retinal, hand-, and eye-related signals on neural activity. The tasks used consisted of 1) reaching to foveated and 2) to extra-foveal targets, with constant eye position; and 3) saccadic eye movement toward, and holding of eye position on peripheral targets, the same as those of the reaching tasks. In all tasks, hand and/or eye movements were made from a central position to eight peripheral targets. A conventional visual fixation paradigm was used as a control task, to assess location and extent of visual receptive field of neurons. A large proportion of cells in area PEc displayed significant relationships to hand movement direction and position. Many of them were also related to the eye's position. Relationships to saccadic eye movements were found for a smaller proportion of cells. Most neurons were tuned to different combination of hand- and eye-related signals; some of them were also influenced by visual information. This combination of signals can be an expression of the early stages of the composition of motor commands for different forms of visuomotor coordination that depend on the integration of hand- and eye-related information. These results assign to area PEc, classically considered as a somatosensory association cortex, a new visuomotor role.

Early coding of reaching in the parietooccipital cortex

Neural activity was recorded in the parietooccipital cortex while monkeys performed different tasks aimed at investigating visuomotor interactions of retinal, eye, and arm-related signals on neural activity. The tasks were arm reaching 1) to foveated targets; 2) to extrafoveal targets, with constant eye position; 3) within an instructed-delayed paradigm, under both light and darkness; 4) saccadic eye movements toward, and static eye holding on peripheral targets; and 5) visual fixation and stimulation. The activity of many cells was modulated during arm reaction (68%) and movement time (58%), and during static holding of the arm in space (64%), when eye position was kept constant. Eye position influenced the activity of many cells during hand reaction (45%) and movement time (51%) and holding of hand static position (69%). Many cells (56%) were also modulated during preparation for hand movement, in the delayed reach task. Modulation was present also in the dark in 59% of cells during this epoch, 51% during reaction and movement time, and 48% during eye/hand holding on the target. Cells (50%) displaying light-dark differences of activity were considered as related to the sight and monitoring of hand motion and/or position in the visual field. Saccadic eye movements modulated a smaller percentage (25%) of cells than eye position (68%). Visual receptive fields were mapped in 44% of the cells studied. They were generally large and extended to the periphery of the tested (30 degrees ) visual field. Sixty-six percent of cells were motion sensitive. Therefore the activity of many neurons in this area reflects the combined influence of visual, eye, and arm movement-related signals. For most neurons, the orientation of the preferred directions computed across different epochs and tasks, therefore expression of all different eye- and hand-related activity types, clustered within a limited sector of space, the field of global tuning. These spatial fields might be an ideal frame to combine eye and hand signals, thanks to the congruence of their tuning properties. The relationships between cell activity and oculomotor and visuomanual behavior were task dependent. During saccades, most cells were recruited when the eye moved to a spatial location that was also target for hand movement, whereas during hand movement most cells fired depending on whether or not the animal had prior knowledge about the location of the visual targets.

Early coding of reaching: frontal and parietal association connections of parieto-occipital cortex

The ipsilateral association connections of the cortex of the dorsal part of the rostral bank of the parieto-occipital sulcus and of the adjoining posterior part of the superior parietal lobule were studied by using different retrograde fluorescent tracers. Fluoro-Ruby, Fast blue and Diamidino yellow were injected into visual area V6A, and dorso-caudal (PMdc, F2) and dorso-rostral (PMdr, F7) premotor cortex, respectively. The parietal area of injection had been previously characterized physiologically in behaving monkeys, through a variety of oculomotor and visuomanual tasks. Area V6A is mainly linked by reciprocal projections to parietal areas 7m, MIP (medial intraparietal) and PEa, and, to a lesser extent, to frontal areas PMdr (rostral dorsal premotor cortex, F7) and PMdc (F2). All these areas project to that part of the dorsocaudal premotor cortex that has a direct access to primary motor cortex. V6A is also connected to area F5 and, to a lesser extent, to 7a, ventral (VIP) and lateral (LIP) intraparietal areas. This pattern of association connections may explain the presence of visually-related and eye-position signals in premotor cortex, as well as the influence of information concerning arm position and movement direction on V6A neural activity. Area V6A emerges as a potential 'early' node of the distributed network underlying visually-guided reaching. In this network, reciprocal association connections probably impose, through re-entrant signalling, a recursive property to the operations leading to the composition of eye and hand motor commands.