Journal: Blood Advances

Article Title: Acute myeloid leukemia–induced remodeling of the human bone marrow niche predicts clinical outcome

doi: 10.1182/bloodadvances.2020001808

Figure Lengend Snippet: AML infiltration induces proliferation of bone marrow MSPCs. (A) Exemplary procedure for quantification of CD271. First, tile images were fused into larger images (1). Second, a color deconvolution was performed (ImageJ, IHC Profiler plugin) to obtain separate hematoxylin and DAB images. The hematoxylin image was thresholded to obtain a mask of the total bone region (2). The DAB image (3) was inverted and thresholded to obtain a mask of the positive DAB regions (4). Scale bars, 1 mm. (B) Representative images of bone marrow biopsy samples of non-leukemic donors (controls) and AML patients stained for CD271+ MSPCs (brown) and counterstained with hematoxylin (blue). Scale bars, 400 µm. (C) Quantification of CD271+ bone marrow MSPCs in controls (n = 58) and AML patients (n = 36); CD271+ area is calculated by CD271+ stained area divided by total tissue surface. (D) Left: representative image from bone marrow after silver staining representing reticular fibers. Right: image converted by trainable Weka segmentation showing 3 different classes: red, reticular fiber; green, tissue; purple, background. Scale bars, 50 µm. (E) Representative images of bone marrow biopsy samples from controls and AML patients stained for reticular fibers with silver staining (black fiber) and counterstained with the fast-red nuclear solution. Scale bars, 100 µm. (F) Quantification of reticular fibers in control (n = 19) and AML (n = 37) bone marrow by calculating positive silver stained area divided by total tissue surface (n = 56). Data are shown as mean ± standard error of the mean (SEM). *P < .05; **P < .01 (determined by Mann-Whitney U test).

Article Snippet: Color deconvolution of the images was performed to obtain separate hematoxylin and DAB images using the ImageJ plugin IHC Profiler ( https://sourceforge.net/projects/ihcprofiler/ ).

Techniques: Staining, Silver Staining, Control, MANN-WHITNEY

Journal: Viruses

Article Title: HIV RGB: Automated Single-Cell Analysis of HIV-1 Rev-Dependent RNA Nuclear Export and Translation Using Image Processing in KNIME

doi: 10.3390/v14050903

Figure Lengend Snippet: NR-SAT single-cell segmentation and tracking scheme. (Phase 1) The input nuclear channel is illumination-corrected using background subtraction, followed by local contrast enhancement. The resulting images then undergo thresholding (Mean method) and are dilated and then labeled. An object filter is applied to remove threshold artifacts prior to converting the images into binary images and filling holes. Finally, the data is passed to the Wählby Cell Clump Splitter, which separates nuclei that are in proximity to one another. (Phase 2) These data are then passed to the nuclei tracking nodes where the ImageJ plugin TrackMate is implemented to track each cell, accounting for splitting and merging events. (Phase 3) After the nuclei are tracked, the nuclear mask is duplicated and dilated (number of dilations is user-defined and applied to all images in the same manner, 10× in this example) to generate two masks, where the newly dilated mask is larger than the original source mask. These two masks (the newly larger dilated mask and the smaller original mask) are then segmented via the Voronoi segmentation node, generating cytoplasmic rings that are approximately a fixed pixel-width. (Phase 4) Finally these cytoplasmic rings, along with the nuclear masks, are applied to the measurement channel(s) and written to a CSV output file.

Article Snippet: NR-SAT represents an intuitive open-source method for single-cell tracking, reliable nucleus vs. cytoplasm cell segmentation, and fluorescence intensity measurements using ImageJ plugins [ , ] integrated into the open source KNIME analytics platform [ ].

Techniques: Labeling