MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

Highly multiplexed tissue imaging makes detailed molecular analysis of single cells possible in a preserved spatial context. However, reproducible analysis of large multichannel images poses a substantial computational challenge. Here, we describe a modular and open-source computational pipeline, MCMICRO, for performing the sequential steps needed to transform whole-slide images into single-cell data. We demonstrate the use of MCMICRO on tissue and tumor images acquired using multiple imaging platforms, thereby providing a solid foundation for the continued development of tissue imaging software.

Minerva: a light-weight, narrative image browser for multiplexed tissue images

Advances in highly multiplexed tissue imaging are transforming our understanding of human biology by enabling detection and localization of 10-100 proteins at subcellular resolution (Bodenmiller, 2016). Efforts are now underway to create public atlases of multiplexed images of normal and diseased tissues (Rozenblatt-Rosen et al., 2020). Both research and clinical applications of tissue imaging benefit from recording data from complete specimens so that data on cell state and composition can be studied in the context of overall tissue architecture. As a practical matter, specimen size is limited by the dimensions of microscopy slides (2.5 × 7.5 cm or ~2-8 cm2 of tissue depending on shape). With current microscopy technology, specimens of this size can be imaged at sub-micron resolution across ~60 spectral channels and ~106 cells, resulting in image files of terabyte size. However, the rich detail and multiscale properties of these images pose a substantial computational challenge (Rashid et al., 2020). See Rashid et al. (2020) for an comparison of existing visualization tools targeting these multiplexed tissue images.

Elimination diets in the treatment of secretory otitis media

The significance of elimination diets in the treatment of secretory otitis media (SOM) and the usefulness of the cytotoxic leucocyte test (CLT) in the planning of elimination diets were investigated. Sixty-seven children with SOM were tested with CLT and treated with or without elimination diets in addition to the established SOM-treatment. After two years of observation in patients with multiple CLT-reactions (50) there was an almost significant difference (P less than 0.06) in the cure rates and a significant difference (P less than 0.02) in the percentages of therapeutic failures between those treated with (32) and those treated without (18) elimination diets. No marked difference was found between patients, who did not have multiple CLT-reactions (17) and were treated without diets and patients who were treated with diets for multiple CLT-reactions (32). It was concluded that elimination diets are needed in the treatment of SOM for those patients who have multiple reactions in the CLT and that the CLT is useful in the planning of these elimination diets.

Reactions in the cytotoxic leucocyte test

A short summary of the literature about the cytotoxic leucocyte test was presented. The results of 1824 CLTs involving 23 food allergens were analyzed. Of the foods tested malt, orange, rye, milk, corn, tomato, oats, wheat, brewers yeast and rice were the ten foods giving a reaction most often in the CLT. Except for minor differences the foods were the same as earlier reported to cause reactions most frequently. Age was found to influence the results of the CLT as cow milk caused reactions most frequently with children and while malt with adults. In 92.1% of the tests there was at least one reaction which means that the CLT is quite sensitive. Thus the CLT seems to be mainly useful for the screening of foods suspected to cause symptoms before planning elimination and provocation trials for the diagnosis of food allergy.

Secretory otitis media and allergy. With special reference to the cytotoxic leucocyte test

This study is an investigation on whether allergy, and especially food allergy, is more common in patients with secretory otitis media (SOM) than in others. At the same time, the effectiveness of the cytotoxic leucocyte test (CLT) as an aid in the diagnosis of food allergy was also studied. The material comprised 90 patients: 69 suffering from secretory otitis media and 21 without the disease as controls. Patients were studied using allergy history, ear status, tests for nasal and blood eosinophilic cells, total IgE, skin tests for 20 allergens. RAST for milk and wheat, immunoglobulin A, G and M, precipitating antibodies for milk and gluten. Mantoux test, and the CLT for 23 allergens. Allergy was found in 20% of the SOM patients and 10% of the control patients; the difference was not statistically significant. The best methods for verifying allergy were history, skin tests, and tests for nasal eosinophils cells. Laboratory tests could not verify objectively that food allergy was more common among SOM patients than controls, although 16% of the SOM patients compared with none of the controls had a history of food allergy. Of the tests used, the CLT correlated best with a history of allergy, but the results of the different tests were not in accordance wtih each other.

Cytotoxic leukocyte reaction

Blood samples from 49 subjects were submitted to cytotoxic leukocyte tests, which were read double-blind by two laboratory technicians. The results were identical in 78% of the tests and the statistical error of the method was 0.46. In a group of 32 subjects, the cytotoxic test was repeated on 3 consecutive days. Deviations in the results occurred in 18--20% of the tests, the statistical errors varying between 0.38 and 0.43. In a series of serum samples (75 subjects) with positive leukocyte reactions to food antigens, various in vitro procedures were carried out in connection with the cytotoxic test. The following observations were made: In 42 of 58 tests, a positive leukocyte reaction was transferred with the reactive serum to cells from non-reactive subjects. After heating of the reactive serum (56 degrees C, 2 h) and washing of the cells, reactivity was no longer observable in 44 out of 52 tests. Treatment with EDTA consistently blocked expected cytotoxic reactions in 36 tests. DSCG inhibited expected reactions in 45%, antihistamine in 93%, and cortisone in 20% of the tests.

Adenoids and otitis media with effusion

At adenoidectomy specimens for bacteriological, virological, and histological investigation were obtained from the adenoids of 144 children, 53 of whom suffered from otitis media with effusion, or frequently recurring otitis media. Comparison of findings in children with ear diseases with those obtained in the rest of the material showed that Hemophilus influenza was cultured from 50% of the specimens from the children with ear diseases, while only 14% of the cultures from the other children yielded H. influenza. Virus isolates were made from 17 adenoids. In children with ear diseases a virus was isolated from 28% of the specimens, whereas positive isolates were obtained in only 3% of the rest of the speciemens. Both findings are statistically significant and support the view that the adenoid tissue may play an important role in the etiology of otitis media with effusion. The infected adenoid may be the direct source of the primary infections, or continuous microbial irritation in the nasopharynx may indirectly be the cause of otitis media with effusion, as persistent infection and edema maintain chronic dysfunction of the eustachian tube. Thus adenoidectomy may be beneficial in the treatment of frequently recurring otitis media, preventing otitis media with effusion from developing.