AnnotateAnyCell: Open-Source AI Framework for Efficient Annotation in Digital Pathology

bioRxiv (Cold Spring Harbor Laboratory) · 2025-11-03

A bstract Manual annotation of histopathological whole slide images remains a critical bottleneck for computational pathology and clinical AI deployment, requiring prohibitive expert time at scale. Here we present an open-source semi-supervised framework combining active contrastive learning with iterative human-in-the-loop feedback for efficient cellular annotation and classification. The pipeline integrates Cellpose segmentation, UMAP-based latent space visualization, and contrastive learning with pseudolabel propagation, evaluated on five whole slide images of canine invasive urothelial carcinoma across low, intermediate, and high histological grades at 40× magnification. Latent space clustering-guided annotation required 47 minutes compared to 63 minutes for sequential annotation, a 25% reduction (95% CI 18–32%). Classification accuracy reached 96.3% ± 1.2% for mitotic figures and 98.3% ± 1.4% for nucleoli using 1,075 labeled samples, with nucleoli classification achieving 95.5% ± 1.5% accuracy from only 215 samples. Inter-annotator agreement was high for chromatin ( κ = 1.00) and nucleoli ( κ = 0.95) but moderate for mitotic figures ( κ = 0.58) and nuclear shape ( κ = 0.36), reflecting intrinsic morphological ambiguity in these categories. This framework substantially reduces annotation burden while achieving expert-level accuracy for well-defined morphological features, providing a scalable path toward AI-assisted diagnostics in resource-constrained pathology settings.

Spatial responses of black vultures to resource pulses during white‐tailed deer hunting seasons

Wildlife Society Bulletin · 2025-04-03 · 1 citations

Abstract Pulsed resources can dramatically influence spatial ecology of wildlife. Black vulture ( Coragyps atratus ) movements depend on habitat structure and foraging opportunities, but their responses to pulsed resources are poorly understood. In contrast, changes to home ranges during large‐game hunting seasons are well documented in mammalian predators. Thus, we hypothesized that increased access to carrion would decrease black vulture space use. To test for changes in space use, we quantified home ranges using data from 12 GPS‐tagged black vultures during nonhunting, archery‐only, and firearms study periods in Indiana and Kentucky, USA. We compared estimated home range size, home range overlap, density of forest edge, and density of roads within each home range. Home range sizes decreased 52.9% from the nonhunting to archery‐only period ( t 35 = 2.77, P = 0.024), then remained stable (increased 9.98%, t 35 = −0.25, P = 0.967) throughout the firearms period. Home range overlaps decreased with greater resource pulse intensities. Estimated forest edge and road densities within home ranges did not change across study periods. Black vultures in our study area changed space use in response to pulsed resources associated with deer hunting. Thus, vultures may shift space use in response to other resource pulses, such as afterbirth and stillbirths from livestock. Pulsed resource locations can serve as targeted survey sites for estimating scavenger abundance and distribution. Integrating resource pulse dynamics into wildlife management strategies can improve efforts to monitor disease risks at aggregation sites and address ecological challenges arising from human activities.

Cytauxzoonosis in Indiana, USA: a case series of cats infected with <i>Cytauxzoon felis</i> (2018–2022)

Journal of Feline Medicine and Surgery · 2024-05-01 · 3 citations

Case series summary This case series describes six cases involving seven cats naturally infected with Cytauxzoon felis in Indiana, USA. Medical records were retrospectively reviewed and all available information on signalment, history, clinical and diagnostic findings, treatment, outcome and pathology was reported. Cats infected with C felis were domestic shorthairs, were aged between 2 and 9 years and all but one of the cats were male. The seven infected cats originated from five counties in southwestern Indiana. Six of seven cats were found to have acute cytauxzoonosis based on clinical signs, gross pathologic lesions, observation of C felis in tissues and/or detection of C felis DNA. One cat was identified as a subclinical survivor cat with no known clinical history of cytauxzoonosis. Relevance and novel information The reported cases are the first confirmed reports of acute and chronic cytauxzoonosis in cats from Indiana and document an expansion in the range of C felis. Veterinary practitioners in Indiana should consider infection with C felis as a differential diagnosis for cats that present with fever, inappetence, lethargy, depression, dehydration, dyspnea, hemolytic crisis, anorexia or icterus. Administration of approved acaricides to cats currently offers the best protection and control against C felis infection.

Competitive Behaviors between Black Vultures (Coragyps atratus) and Turkey Vultures (Cathartes aura) during Scavenging

Journal of Raptor Research · 2024-09-05 · 5 citations

La competencia por interferencia ocurre cuando un individuo, a través de interacciones antagónicas, limita el acceso de otro a un recurso. A pesar de que existe una cantidad considerable de investigaciones sobre las interacciones de los carroñeros en presencia de alimento, la poca evidencia de interacciones competitivas entre Coragyps atratus y Cathartes aura se basa en la frecuencia de interacciones antagónicas, sin considerar otras formas de competencia. Usando cámaras remotas, registramos la duración de los comportamientos de agresión, carroñeo y vigilancia exhibidos por individuos de C. atratus y C. aura alimentándose de ganado doméstico natimorto dentro de bandadas compuestas por una o ambas especies de buitres. Evaluamos las diferencias en las duraciones de cada comportamiento según la especie de buitre, la composición de la bandada y el efecto combinado de la especie de buitre y la composición de la bandada. Sorprendentemente, los comportamientos agresivos fueron raros y su duración no difería significativamente según la especie de buitre. Las tendencias más claras entre nuestras comparaciones revelaron que la duración de la agresión fue significativamente más larga para C. atratus en bandadas de una sola especie, mientras que la duración de su alimentación fue más larga en bandadas de especies mixtas. C. aura exhibió tiempos de vigilancia mas largos en presencia de múltiples congéneres y de individuos heteroespecíficos. Nuestros resultados indicaron que C. atratus exhibió más agresión hacia individuos carroñeros congéneres que hacia los heteroespecíficos. Nuestros hallazgos identifican las formas complejas en las que C. atratus compite con C. aura, más allá de la simple agresión. [Traducción del equipo editorial]

Drivers of agricultural producers' tolerance towards less-charismatic avian species

Biological Conservation · 2024-11-29

Increasing wildlife tolerance (i.e., “the willingness of an individual to absorb the extra potential or actual costs of living with wildlife”) can reduce human-wildlife conflict (HWC). Previous research shows how socio-cultural and psychological factors shape HWC, focusing on carnivores and charismatic species. Less-charismatic species, particularly non-mammals, have received less attention from both the scholarly and policy-making communities even though they may be socially, culturally, and ecologically important. This paper applies the Wildlife Tolerance Model (WTM) to examine livestock producers' interactions with a less-charismatic avian species, black vultures ( Coragyps atratus ), in the Midwestern USA, as an example of an emerging HWC in an agricultural landscape. We collected usable survey data from 168 livestock producers in Indiana and Kentucky and used a partial-least squares structural equation model to assess potential drivers of their tolerance of black vultures. Intangible costs (i.e., negative emotions associated with black vultures), utilitarian wildlife value orientations (WVOs), and tendency towards using more severe management actions were significantly associated with reduced tolerance. Intangible benefits (i.e., “non-monetary factors such as stress and fear”) and mutualistic WVOs were significantly associated with increased tolerance. Importantly, tangible costs (i.e., “estimated economic costs associated with livestock losses due to wildlife predation”) were not a significant predictor of black vulture tolerance. This paper highlights the importance of socio-cultural and psychological factors, rather than economic factors, in shaping people's tolerance of a less-charismatic avian species. It demonstrates the utility of WTM as a framework for assessing the economic, socio-cultural, and psychological drivers of less-charismatic avian species. • Negative emotions and utilitarian WVOs lower black vulture tolerance. • Perceived ecological values and mutualistic WVOs increase black vulture tolerance. • Perceived economic losses is not a significant predictor of black vulture tolerance. • Socio-psychological factors, more than economic factors, shape black vulture tolerance. • The Wildlife Tolerance Model is useful for assessing tolerance of less charismatic species.

Taphonomic signatures of early scavenging by black and turkey vultures

PLoS ONE · 2024-08-14 · 6 citations

Scavenging is critical for nutrient cycling and maintenance of healthy ecosystems. While there is substantial research into the identification of taphonomic signatures from facultative mammalian scavengers, early stage scavenging signatures by vultures remain unknown. Further, some vulture species are opportunistic predators, highlighting the need to define signatures observed in the course of normal scavenging behavior. We placed stillborn neonatal calves in an unoccupied pasture and used motion-trigger camera traps to quantify scavenging effort, then conducted necropsies to evaluate the effect of black vulture (Coragyps atratus) and turkey vulture (Cathartes aura) scavenging effort on carcass consumption. We measured the order of consumption of different tissue types to delineate which anatomic structures vultures consume first. Scavenging trials with higher numbers of vultures feeding on the carcass for longer were associated with decreased remaining tongue and abdominal viscera, and a larger umbilical wound. Greater maximum flock sizes were associated with decreased remaining tongue and abdominal viscera, a larger umbilical wound, and greater biomass consumption. Black vultures targeted the perineum and tongue earlier, while turkey vultures targeted the eyes, perineum, and tongue. These results are consistent with the idea that vultures prefer tissues that are easy to access and contain high nutrient content. These patterns form a distinctive taphonomic signature that can be used to identify early scavenging by black and turkey vultures. Our results demonstrate that criteria commonly used to identify livestock depredation by black vultures only document vulture presence and not predation. This distinction implies that new and more definitive criteria need to be developed and put into practice for more accurate decision criteria in livestock depredation compensation programs.

Supplemental Figure 2 from Cholesterol Sulfonation Enzyme, SULT2B1b, Modulates AR and Cell Growth Properties in Prostate Cancer

2023-04-03

&lt;p&gt;Modulation of SULT2B1b alters relative abundance of CS in LNCaP cells.&lt;/p&gt;

Data from Cholesterol Sulfonation Enzyme, SULT2B1b, Modulates AR and Cell Growth Properties in Prostate Cancer

2023-04-03

&lt;div&gt;Abstract&lt;p&gt;Cholesterol accumulates in prostate lesions and has been linked to prostate cancer incidence and progression. However, how accumulated cholesterol contributes to prostate cancer development and progression is not completely understood. Cholesterol sulfate (CS), the primary sulfonation product of cholesterol sulfotransferase (SULT2B1b), accumulates in human prostate adenocarcinoma and precancerous prostatic intraepithelial neoplasia (PIN) lesions compared with normal regions of the same tissue sample. Given the enhanced accumulation of CS in these lesions, it was hypothesized that SULT2B1b-mediated production of CS provides a growth advantage to these cells. To address this, prostate cancer cells with RNAi-mediated knockdown (KD) of SULT2B1b were used to assess the impact on cell growth and survival. SULT2B1b is expressed and functional in a variety of prostate cells, and the data demonstrate that SULT2B1b KD, in LNCaP and other androgen-responsive (VCaP and C4-2) cells, results in decreased cell growth/viability and induces cell death. SULT2B1b KD also decreases androgen receptor (AR) activity and expression at mRNA and protein levels. While AR overexpression has no impact on SULT2B1b KD-mediated cell death, the addition of exogenous androgen is able to partially rescue the growth inhibition induced by SULT2B1b KD in LNCaP cells. These results suggest that SULT2B1b positively regulates the AR either through alterations in ligand availability or by interaction with critical coregulators that influence AR activity.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Implications:&lt;/b&gt; These findings provide evidence that SULT2B1b is a novel regulator of AR activity and cell growth in prostate cancer and should be further investigated for therapeutic potential. &lt;i&gt;Mol Cancer Res; 14(9); 776–86. ©2016 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;

Supplemental Figure 4 from Cholesterol Sulfonation Enzyme, SULT2B1b, Modulates AR and Cell Growth Properties in Prostate Cancer

2023-04-03

&lt;p&gt;shRNA KD of SULT2B1b expression yields similar results to siRNA KD.&lt;/p&gt;

Science‐driven guidelines needed to better manage and conserve black vultures in North America

Wildlife Letters · 2023 · 5 citations

• Geography
• Environmental resource management
• Ecology

Abstract Black vultures ( Coragyps atratus ) provide invaluable ecological services through disposal of carrion and the mobilization of energy within the landscape. Human‐wildlife conflicts with these birds have increased as populations have grown and the species distribution has expanded. We identify critical science needed to understand conflict between black vultures and humans to inform effective management of this species in North America. It is imperative that diagnostic criteria supporting the identification of the impacts of black vulture on livestock be standardized and verified. Management guidelines that take these criteria into account will enable reduction in the potential for black‐vulture‐farmer conflict and allow us to properly investigate such conflict when it occurs.