Journal: Communications Biology

Article Title: Deep-learning deconvolution and segmentation of fluorescent membranes for high-precision bacterial cell-size profiling

doi: 10.1038/s42003-026-10303-y

Figure Lengend Snippet: a Example of deconvolution prediction with FM2FM. Top, input raw fluorescent membrane images (Raw FM 4-64); middle row, true deconvolved fluorescent membrane images (Deconvolved FM 4-64); bottom, FM2FM-predicted image. White squares mark regions zoomed in at right (Block 1 and Block 2). Diagonal dotted lines indicate profile traces in ( b ). Scale bars: full images, 10 µm; zoomed-in blocks, 5 µm. b Fluorescence profiles across the dotted lines in Block 1 (top) and Block 2 (bottom). Light blue, raw FM 4-64; orange, deconvolved FM 4-64; burgundy, FM2FM prediction. c , Structural similarity index measure (SSIM) between FM2FM predicted images and deconvolved images. The distribution of SSIM values across 74 image crops is shown. d Violin plots of cell width, length, surface area, volume, cross-sectional area, convex hull area, eccentricity and solidity calculated from deconvolved FM 4-64 images (orange) and FM2FM-predicted images (burgundy). The white dots and vertical lines within the violin plots represent the medians and standard deviations. P values from statistical comparisons between distributions (ANOVA or Kruskal test; see methods for details) are indicated in each panel. Twenty images (over 1000 cells) were processed and segmented with FMSeg. See the Methods for size calculation details.

Article Snippet: To compare model performance against the membrane deconvolution target (SoftWorx), we conducted qualitative assessments of output images' intensity profiles.

Techniques: Membrane, Blocking Assay, Fluorescence

Journal: bioRxiv

Article Title: Novel mouse reporter models for the detection of genome editing events in vivo

doi: 10.64898/2026.04.29.721708

Figure Lengend Snippet: a) Schematic of TLR-2 reporter allele structure and outcomes following editing. The allele includes two open reading frames encoding different fluorescent proteins; an upstream mVenus (green) in the +1 frame and downstream TagRFP (red) in the +3 frame linked by a P2A sequence. The mVenus cassette is interrupted by a 108 bp polylinker sequence that includes several guide target sequences and a stop codon (blue square). Thus in its native configuration, neither fluorescent protein is expressed. Following CRISPR/Cas9 editing, repair via NHEJ will result in expression of TagRFP if the frame shift results in a -2 deletion, or multiple thereof. Alternatively, HDR can be detected with the inclusion of a plasmid donor designed to repair the mVenus gap. b) Mouse embryo reporter validation workflow. Fertilized zygotes from TLR-2 reporter mice (typically male homozygous to WT female) are either microinjected or electroporated with Cas9 RNP with or without a plasmid donor for HDR. The embryos are then cultured to the blastocyst stage where the outcome can be scored by fluorescent imaging, and followed up by PCR-Sanger sequencing to confirm the identify of specific edits.

Article Snippet: Sanger sequence traces were analyzed using the ICE (Inference of CRISPR Editing) deconvolution tool from Synthego. ( https://ice.synthego.com ; Synthego Performance Analysis, ICE Analysis.

Techniques: Sequencing, CRISPR, Expressing, Plasmid Preparation, Biomarker Discovery, Cell Culture, Imaging