Journal: bioRxiv

Article Title: cloneXplorer: A high-throughput clone discovery platform based on conical microwell arrays

doi: 10.64898/2026.01.16.699323

Figure Lengend Snippet: Measurements of single cell proliferation. (a) An overview of the image analysis pipeline is provided. (b) The mean and standard deviation of the number of microwells with 1, 2, 3, and 4+ cells are shown. The percentages are calculated relative to the ∼2,800 microwells imaged per well. (c) Boxplot shows the cell division rates for each well of the plate. In total, the growth measurements for 93,081 microwells containing a single NALM6 cell at the initial timepoint is reported. (d) The fraction of proliferating T cells in two donor samples (Donor 1 and 2) is plotted versus activation matrix (T = Miltenyi Transact CD3/CD28, D = ThermoFisher Dynabeads CD3/CD28) and human AB serum percentage. The mean values for n=4 wells are shown with error bars representing the standard deviation. (e) The mean percentage of viable clones at 90 hours and their standard deviations are shown for donor T cells exposed to different levels of fluorescent light, including 390 nm excitation for 0.05s (short blue) or 0.2s (long blue) exposure, and 565 nm excitation for 0.8s (short red) or 3.2s (long red) exposures. Microwells loaded with a single T cell are shown and viable clones are defined as T cells that divided at least once. (f) Violin plot showing the clone size distribution in terms of the number of cells per microwell for the same conditions as (e). Scale bar is 50 μm.

Article Snippet: The activation dynamics of freshly thawed human T cells exposed to different CD3/CD28 activation matrices (Miltenyi Transact vs ThermoFisher Dynabeads) in different media (AIM V vs TexMACS) and supplemented with different levels of human serum (0%, 1%, 5%) is shown as a map of cell counts imaged at 3 hour intervals for 130 hours.

Techniques: Standard Deviation, Activation Assay, Clone Assay

Journal: bioRxiv

Article Title: cloneXplorer: A high-throughput clone discovery platform based on conical microwell arrays

doi: 10.64898/2026.01.16.699323

Figure Lengend Snippet: Cell growth distribution for freshly thawed T cells exposed to different levels of human serum (0%, 1%, 5%), different methods of CD3/CD28 stimulation (Dynabeads vs Transact), and different media conditions (TexMACS vs AIM V). The gray level indicates the cell count at 142 hr on a scale of 0 (black) to 100 (white).

Article Snippet: The activation dynamics of freshly thawed human T cells exposed to different CD3/CD28 activation matrices (Miltenyi Transact vs ThermoFisher Dynabeads) in different media (AIM V vs TexMACS) and supplemented with different levels of human serum (0%, 1%, 5%) is shown as a map of cell counts imaged at 3 hour intervals for 130 hours.

Techniques: Cell Characterization

Journal: bioRxiv

Article Title: cloneXplorer: A high-throughput clone discovery platform based on conical microwell arrays

doi: 10.64898/2026.01.16.699323

Figure Lengend Snippet: (a) The overall workflow is illustrated. (b-c) Flow cytometric plots of T cells stained with anti-CD8 antibody and MART1 tetramer after enrichment with either MART1 peptide (b) or DMSO (c). (d) Number of IFN-γ+ microwells per well, with color denoting the condition: T cells with anti-CD3/CD28 antibodies (blue, positive control), T cells with DCs and MART1 peptide (red), T cells with unpulsed DCs (green), T cells with MART1 peptide (purple), T cells (orange), DCs or no cells. (e) Hierarchical gating strategy to identify microwells with an IFN-γ signal (left), containing proliferating cells (center) and CD8-positive cells (right). (f) Example of one clone pick. Left panel: Images of a selected microwell at multiple time points in brightfield (BF) and fluorescence (IFN-γ and CD8) channels. BF is used to assess initial conditions (−1 h: 1 T cell loaded, 0 h: additionally 2 DCs loaded) as well as growth rate. Right panel: Images of the array before picking and after picking are shown in all channels. The disappearance of cells after picking is noticeable in the CD8 channel. (g) Flow cytometry plot of the cells picked in (f) that were further expanded before analysis.

Article Snippet: The activation dynamics of freshly thawed human T cells exposed to different CD3/CD28 activation matrices (Miltenyi Transact vs ThermoFisher Dynabeads) in different media (AIM V vs TexMACS) and supplemented with different levels of human serum (0%, 1%, 5%) is shown as a map of cell counts imaged at 3 hour intervals for 130 hours.

Techniques: Staining, Positive Control, Fluorescence, Flow Cytometry