DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes

Deep learning is transforming the analysis of biological images, but applying these models to large datasets remains challenging. Here we describe the DeepCell Kiosk, cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets. To demonstrate the scalability and affordability of this software, we identified cell nuclei in 10⁶ 1-megapixel images in ~5.5 h for ~US$250, with a cost below US$100 achievable depending on cluster configuration. The DeepCell Kiosk can be downloaded at https://github.com/vanvalenlab/kiosk-console; a persistent deployment is available at https://deepcell.org/

DeepCell Kiosk: scaling deep learning–enabled cellular image analysis with Kubernetes

Deep learning is transforming the analysis of biological images, but applying these models to large datasets remains challenging. Here we describe the DeepCell Kiosk, cloud-native software that dynamically scales deep learning workflows to accommodate large imaging datasets. To demonstrate the scalability and affordability of this software, we identified cell nuclei in 10⁶ 1-megapixel images in ~5.5 h for ~US$250, with a cost below US$100 achievable depending on cluster configuration. The DeepCell Kiosk can be downloaded at https://github.com/vanvalenlab/kiosk-console; a persistent deployment is available at https://deepcell.org/

<b>Catalytic STEREOSELECTIVE </b>β<b>–Elimination Reactions using Cobalt Vinylidenes</b>

Ring strain is the driving force for numerous ring-opening reactions of three- and four-membered heterocycles. By comparison, five-membered heterocycles lack this thermodynamic driving force. As a result, only a few methods exist for the ring-opening of five-membered heterocycles using transition metal catalysts. For unstrained and unactivated 2,5-dihydrofurans this is achieved via a β-O elimination process, wherein, gaining selectivity over a competing β-H elimination is challenging. We report a novel strategy for the asymmetric ring-opening of 2,5-dihydrofurans with dichloroalkenes utilizing an earth-abundant cobalt catalyst. We propose that the dichloroalkenes form reactive vinylidene intermediates with the chiral catalyst, followed by a [2+2] cycloaddition with the heterocyclic alkene. This cobaltacyclobutane exclusively undergoes an outer-sphere β-O elimination assisted by zinc halide. Alternative inner-sphere β-O and β-H elimination pathways are inaccessible from this four-membered metallacycle. This is followed by a transmetallation step to form a zinc metallacycle, which subsequently gives rise to homoallylic alcohols, upon quenching, with high diastero- and enantioselectivity. Additionally, the organozinc intermediate can be trapped in situ by various electrophiles for further derivatizations. DFT model predicts the origin of the high diastereo- as well as enantioselectivity observed in the reaction.Furthermore, the cobaltacyclobutane intermediate serves as a dynamic platform, facilitating access to a diverse array of products depending on the alkene partners employed. Utilizing chiral allylic alcohols as alkene partners leads to the translation of stereochemical information enabling the stereospecific synthesis of both E- and Z-isomers of alkenes. Alkenes are important motifs found in various natural products and bioactive compounds. A catalytic approach for the precise control of the alkene geometry is highly valuable since the stereochemistry of alkenes plays a pivotal role in determining the properties of molecules. Our strategy provides access to organozinc dienes which could be functionalized further to form highly substituted 1,4-skipped dienes. Additionally, meso-diols can undergo a desymmetrizing β-O elimination from the cobaltacyclobutane intermediate yielding chiral cyclopentenols with contiguous stereocenters</p