Images were collected using our custom-built STORM system on both formalin-fixed, paraffin-embedded (FFPE) tissue section and cultured cells. The imaging systems, sample preparation, image acquisition and reconstruction have been previously described [5, 7]. The image characteristics of cell nuclei can vary dramatically depending on the labeled targets. We included a diverse set of STORM images of nuclei with different molecular targets that exhibit various distinct nuclear textures (e.g., discrete clusters, diffuse pattern, or dense clumps) from the various labeled molecular targets from different biological or pathological states. Additional file 8: Table S1 shows the list of cell/tissue types, labeled target in the nuclei, biological or pathological states of the cells or tissue and fluorophore used.

All STORM-based super-resolution images were originally captured at 5120 × 5120 pixels, and were resized for speed during training. Downsizing was conducted using bilinear interpolation with averaging. Datasets were constructed by creating 1024 × 1024, 512 × 512 and 256 × 256 versions of the STORM images of cell nuclei from human colon tissue as well as 512 × 512 and 256 × 256 versions of the STORM images of cell nuclei from cell lines.

Additional datasets were created for training and testing by blurring or contrast enhancing the STORM images of nuclei from human colon tissue and cell lines with resized 512 × 512 and 256 × 256 datasets. Blurring was applied using a Gaussian filter with sigma set at 2. Contrast enhancement was conducted by means of histogram equalization with normalization, to limit intra image variations. All image resizing and pre-processing steps described in this section were conducted using Fiji [39]. Our workflow is depicted in Fig. 8.

Workflow for STORM image acquisition, labeling, processing, network training and testing. Sequence begins at the top left and proceeds clockwise

A total of 134 STORM images of nuclei labeled with heterochromatin marker (H3K9me3) were included in the human colon tissue dataset, of which 60% were used for training, 30% for testing and 10% for validation. The same testing, training and validation images were used for each network. Additionally, a set of 69 STORM images of nuclei stained with the same marker from mouse prostate tissue (from Myc-driven prostate tumorigenesis mouse model and wild-type mice) were used as an alternate test set for the network models trained on colon tissue data. These datasets include normal tissue and those at different pathological states (low-grade and high-grade precancerous lesions and invasive cancer). As we have previously shown, chromatin compaction becomes progressively more disrupted in carcinogenesis and therefore chromatin texture varies significantly in normal tissue, precancerous lesions, and invasive cancer [7].

Two training sets were collected for the cell line dataset. Cell lines used in this dataset include mouse and human fibroblast cells, human breast cancer cells, kidney cells and prostate cancer cells. A wide variety of molecular targets in the cell nuclei (H3K27me3, H3K4me3, DNA, RNA polymerase II) were labeled, which are characteristic of a diverse “texture” of nuclear organization. These datasets were generally divided into two categories based on its image characteristics: discrete and dense nuclear texture, which depend on either molecular targets or biological states. A total of 44 STORM images with discrete nuclear texture and an additional 65 images with dense nuclear texture were used in this study. Each dataset was divided: 60% for training, 30% for testing and 10% for validation. The STORM images of cell nuclei with discrete nuclear texture comprised our first, single-source (single labeled target of RNA polymerase II) cell line training and validation dataset (Additional file 9: Figure S8), herein referred to as cell line dataset A. Next, the STORM image training and validation datasets including images with both discrete and dense nuclear texture comprised our second, multiple-source (i.e., various labeled targets) training and validation set, which we shall call cell line dataset B. Then, the two test sets from cell line datasets A & B were combined to create a single test dataset for both the discrete and dense nuclear texture cell line training sets. In this way, we directly compared the network performances of both models: trained on a single data source presenting a discrete texture, versus trained on multiple sources containing both discrete and dense texture. A more complete breakdown of cell type, biological state, labeled molecular target and fluorophore used in each image set, as well as a breakdown of which dataset each image type appears in (Additional file 8: Table S1).

In addition to our own STORM super-resolution image dataset, we also trained and tested our selection of neural networks using the 2018 Kaggle data science bowl dataset [1]. Included in this publicly available nuclear image dataset were wide-field fluorescence, H&E stained and brightfield microscopic images of nuclei from cultured cells and tissue. From the entirety of the dataset, we utilized only the stage 1 training set, containing 670 labeled images. Kaggle datasets were not resized, but rather tested as is.

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