Kyle W. Karhohs's research while affiliated with Broad Institute of MIT and Harvard and other places

... Then, the feature correlation distribution of replicate wells (percent replicating) or MOA matching wells (percent matching) is calculated. The percentage of the replicate or matching distribution that is above the 95th percentile of the null distribution is the percent replicating or percent matching score, respectively [16]. ...

... Patient-specific iPSC-derived neuronal cells can be used for assessing cell-based traits associated with disease-related mutations. Previously, an open-source cloud-based image processing and analysis platform (CELLXPEDITE) was used to screen compounds that revert the multiparametric disease profile of ALS back to that of healthy motor neurons [235]. This is advantageous when compared to the unidimensional characterisation of other screening methods for diseases such as ALS [236], as it allows for a simultaneous measurement of multiple parameters that would be more reflective of a complex disease. ...

... This equated to an accuracy of 0.52 (random accuracy = 0.006). To assess the influence of well-location effects which are common in microscopy 38,39 , we compared the model's performance on edge wells versus non-edge wells. We found minor differences in classification accuracy (0.54 vs .50) ...

... The analysis in this work is based on two datasets of individual human cells that were published in [23,29]. The cells were monitored using fluorescence live-cell imaging for about a week after being subjected to irradiation. ...

... Unrepaired ICLs lead to a complete block of the separation of the complementary DNA strands and therefore inhibit several essential processes such as DNA replication and transcription [28,30]. If the replication fork stalls at an ICL, it is processed into a double-strand break (DSB), which in turn stops cell cycle progression [28,[31][32][33]. Another consequence of ICLs is that DNA-protein interactions (e.g., transcription factors binding to DNA) at the affected sites of the DNA are no longer possible. ...

... One identified IBA1-positive cells expressing BIN1 in immunohistochemical analysis of post-mortem brain tissue from patients with AD [8]. Another study reported detection of BIN1 isoforms 12 and 6 in the nucleus of CD45 + microglia using antibodies raised against BIN1 exons 11 and 13; notably, the major microglial BIN1 isoform 10 lacking both exons 11 and 13 was not observed by immunostaining in the previous study [65]. In this regard, it is worth mentioning that exon 11, which codes for a polybasic sequence that confers binding to phosphoinositides and is essential for BIN1-induced membrane tubulation [66], is spliced out from Bin1 transcripts in adult mouse brain microglia and human induced iPSCs-derived microglia (Fig. S2A). ...

... 4 In our recent work, we have focused on cell surface area, perimeter, circularity (FormFactor), pseudopodia (endpoint) number, and total pseudopodia length. 1 Examples of the processing steps from which these outputs are measured are seen in Figure 2. Cell morphology characteristics have been shown to change under various conditions, such as chronic stress. 1 Protocols similar to this have also been used in other biological contexts and cell types, demonstrating the broad applicability of quantifying cell morphology. 8,9 Cell morphology phenotypes can be indicative of organism characteristics; for example, differences in cell morphology have been associated with donor age more closely than other established biomolecular measurements such as DNA damage response or adenosine triphosphate content. 10 ...

... Data Science Bowl 2018(DSB2018) [58] includes 670 artificially segmented nuclei images from experiments across different tissue samples, staining protocols, imaging conditions and microscopes. This dataset consists of 29455 manually annotated nuclei boundaries by a team of expert biologists. ...

... Given that ureteral smooth muscle cells (USMCs) cannot be obtained commercially, we cultured USMCs from rats and patient ureters using a de novo technique [14]. Briefly, the ureters harvested from patients and rats were immediately placed in cold Krebs solution, cut into 5 mm sections, and incubated on a plate containing trypsin. ...

... The 2018 data science bowl (DSB) dataset was created as a challenge for generic segmentation of nuclei of cells in a diverse set of stained two-dimensional (2D) microscopic images [9]. The training set contains 670 images from both bright-stained and fluorescence modalities of microscopic images with sizes 256 Â 256 Â 3. In addition to the images captured under various lighting conditions, corresponding annotations (segmentation masks) for each image are also provided to be used as ground truth. ...