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AI Module Delivers Predictive Image Segmentation and Processing

By MedImaging International staff writers
Posted on 23 Dec 2019

Image: A suite of microscopy applications aid predictive imaging, segmentation, and processing (Photo courtesy of Nikon Instruments)

A powerful image analysis and processing module leverages deep learning and artificial intelligence (AI) to accurately extract unbiased data from vast amounts of microscopy datasets.

The Nikon Instruments (Melville, NY, USA) NIS.ai microscopy image analysis and processing module is a suite of AI-based processing tools that utilizes convolutional neural networks (CNNs) in order to learn how to read images from small training datasets supplied by the user. The training results can then be applied to process and analyze huge volumes of data, allowing researchers to increase throughput and expand their application limits. The NIS.ai includes a suite of applications for predictive imaging, image segmentation, and processing. These include:

Convert.ai, which learns related patterns in two different imaging channels. After training, Convert.ai can predict the pattern in the second channel, even when presented with only the first channel. It can also be trained to predict where DAPI-based fluorescent staining of nuclei--a common method for cell segmentation and counting--could be based on unstained differential interference contrast (DIC) or phase-contrast microscopy images. This enables users to perform nuclei-based image analysis without ever having to stain samples with DAPI or acquire a fluorescent channel.

Segment.ai, which enables complex structures to be easily identified and segmented. Neurites in phase-contrast images are traditionally difficult to define by classic thresholding. Segment.ai can be trained on a small subset of hand-traced neurites to automatically detect and segment neurites from thousands of untraced datasets.

Enhance.ai, which allows dim fluorescent samples with poor signal-to-noise ratio (SNR) to be enhanced by learning what a high signal-to-noise image looks like, via a process that compares under-exposed and optimally-exposed images. Enhance.ai can then restore details in under-exposed or dim fluorescent images, enabling researchers to gain more insights from their low-signal imaging applications.

Denoise.ai, which removes shot noise from resonant confocal images and can be performed in real-time. Applying Denoise.ai to resonant confocal imaging enables users to acquire confocal images at ultra-high speed without sacrificing image quality.

“The application of Deep Learning and AI to biomedical imaging is extremely powerful, and opening up unseen possibilities,” said Steve Ross, PhD, director of products and marketing at Nikon Instruments. “With NIS.ai, researchers can easily apply deep learning to extract meaningful, unbiased data from large, complex datasets.”

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70 (292.06275939941): SELECT fid FROM jos_deeppockets WHERE cat=10 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

71 (252.96211242676): SELECT fid FROM jos_deeppockets_archive WHERE cat=10 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

72 (40.054321289062): SELECT id,name,title FROM jos_deeppockets WHERE cat=10 AND TYPE='file_folder' AND published=1 AND id != 294743300 AND id != 294743301 AND id != 294743302 AND id != 294743303 AND id != 294743304 AND id != 294743305 AND id != 294743306 AND id != 294743307 AND id != 294743308 AND id != 294743309 AND id != 294743310 AND metakey != 'aacc' ORDER BY `ordering`

73 (66.995620727539): SELECT show_live FROM jos_com_show_setting LIMIT 1

74 (33.140182495117): SELECT show_live FROM jos_com_show_setting LIMIT 1

75 (28.133392333984): SELECT show_live FROM jos_com_show_setting LIMIT 1

76 (27.894973754883): SELECT show_live FROM jos_com_show_setting LIMIT 1

77 (26.941299438477): SELECT show_live FROM jos_com_show_setting LIMIT 1

78 (27.894973754883): SELECT show_live FROM jos_com_show_setting LIMIT 1

79 (40.054321289062): SELECT show_live FROM jos_com_show_setting LIMIT 1

80 (35.04753112793): SELECT show_live FROM jos_com_show_setting LIMIT 1

81 (40.054321289062): SELECT show_live FROM jos_com_show_setting LIMIT 1

82 (31.948089599609): SELECT show_live FROM jos_com_show_setting LIMIT 1

83 (27.894973754883): SELECT show_live FROM jos_com_show_setting LIMIT 1

84 (28.133392333984): SELECT show_live FROM jos_com_show_setting LIMIT 1

85 (36.001205444336): SELECT show_live FROM jos_com_show_setting LIMIT 1

86 (30.040740966797): SELECT show_live FROM jos_com_show_setting LIMIT 1

87 (46.968460083008): SELECT fid FROM jos_deeppockets WHERE cat=10 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

88 (28.848648071289): SELECT fid FROM jos_deeppockets_archive WHERE cat=10 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

89 (31.948089599609): SELECT id,name,title FROM jos_deeppockets WHERE cat=10 AND TYPE='file_folder' AND published=1 AND id != 294743300 AND id != 294743301 AND id != 294743302 AND id != 294743303 AND id != 294743304 AND id != 294743305 AND id != 294743306 AND id != 294743307 AND id != 294743308 AND id != 294743309 AND id != 294743310 AND metakey != 'aacc' ORDER BY `ordering`

90 (985.86082458496): SELECT show_live FROM jos_com_show_setting LIMIT 1

91 (64.13459777832): SELECT show_live FROM jos_com_show_setting LIMIT 1

92 (42.915344238281): SELECT show_live FROM jos_com_show_setting LIMIT 1

93 (33.140182495117): SELECT show_live FROM jos_com_show_setting LIMIT 1

94 (41.007995605469): SELECT show_live FROM jos_com_show_setting LIMIT 1

95 (39.815902709961): SELECT show_live FROM jos_com_show_setting LIMIT 1

96 (66.995620727539): SELECT show_live FROM jos_com_show_setting LIMIT 1

97 (43.153762817383): SELECT show_live FROM jos_com_show_setting LIMIT 1

98 (56.982040405273): SELECT show_live FROM jos_com_show_setting LIMIT 1

99 (30.994415283203): SELECT show_live FROM jos_com_show_setting LIMIT 1

100 (28.848648071289): SELECT show_live FROM jos_com_show_setting LIMIT 1

101 (29.087066650391): SELECT show_live FROM jos_com_show_setting LIMIT 1

102 (243.9022064209): SELECT show_live FROM jos_com_show_setting LIMIT 1

103 (35.04753112793): SELECT show_live FROM jos_com_show_setting LIMIT 1

104 (565.0520324707): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

105 (53.882598876953): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

106 (69.856643676758): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.cat=10 AND dp.id=294780321 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

107 (53.167343139648): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets_archive as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.cat=10 AND dp.id=294780321 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

108 (!!!!! 3918.1709289551): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

109 (158.07151794434): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

110 (422.00088500977): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.id=294780321 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

111 (490.90385437012): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets_archive as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.id=294780321 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

112 (699.99694824219): SELECT dp.name, dp.id, dp2.name as channel, ex.name as author_name, ex.specialization, ex.images FROM jos_deeppockets as dp LEFT JOIN jos_experts as ex ON ex.id = dp.author LEFT JOIN jos_deeppockets as dp2 ON dp2.id = dp.fid WHERE dp.author != 0 AND dp.cat = 10 AND dp.published = 1 AND ( (dp.fid = 294743300) OR (dp.fid = 294743301) OR (dp.fid = 294743302) OR (dp.fid = 294743303) OR (dp.fid = 294743304) OR (dp.fid = 294743305) OR (dp.fid = 294743306) OR (dp.fid = 294743307) OR (dp.fid = 294743308) OR (dp.fid = 294743309) OR (dp.fid = 294743310) ) ORDER BY RAND() LIMIT 1

113 (391.96014404297): SELECT dp.name, dp.id, dp2.name as channel, ex.name as author_name, ex.specialization, ex.images FROM jos_deeppockets as dp LEFT JOIN jos_experts as ex ON ex.id = dp.author LEFT JOIN jos_deeppockets as dp2 ON dp2.id = dp.fid WHERE dp.author != 0 AND dp.cat = 10 AND dp.published = 1 AND ( (dp.fid = 294743300) OR (dp.fid = 294743301) OR (dp.fid = 294743302) OR (dp.fid = 294743303) OR (dp.fid = 294743304) OR (dp.fid = 294743305) OR (dp.fid = 294743306) OR (dp.fid = 294743307) OR (dp.fid = 294743308) OR (dp.fid = 294743309) OR (dp.fid = 294743310) ) ORDER BY RAND() LIMIT 1

114 (96.08268737793): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

115 (56.982040405273): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

116 (102.99682617188): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

117 (37.908554077148): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

118 (51.021575927734): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

119 (38.14697265625): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

120 (342.84591674805): SELECT * FROM trending_articles WHERE `journal_id` = 10 AND `timestamp` <= NOW() + INTERVAL 7 DAY ORDER BY `order`

121 (!!!!! 22171.020507812): SELECT * FROM jos_deeppockets WHERE jos_deeppockets.cat = 10 AND jos_deeppockets.type = 'deeppockets_item' AND jos_deeppockets.published = 1 AND jos_deeppockets.created + INTERVAL 14 DAY >= NOW() ORDER BY jos_deeppockets.hits DESC LIMIT 7

122 (102.99682617188): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

123 (50.067901611328): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

124 (467.06199645996): SELECT fid FROM jos_deeppockets WHERE cat=10 AND id=294780321 AND type='deeppockets_item' AND published='1' union SELECT fid FROM jos_deeppockets_archive WHERE cat=10 AND id=294780321 AND type='deeppockets_item' AND published='1' LIMIT 1

125 (!!!!! 513326.1680603): ( SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.video != '' AND dp.video_source != '' AND dp.cat = 10 AND dp.published = 1 AND dp.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) UNION ( SELECT dpa.id, dpa.name, dpa.title, dpa.video, dpa.video_source, dpa.created FROM jos_deeppockets_archive AS dpa WHERE dpa.video != '' AND dpa.video_source != '' AND dpa.cat = 10 AND dpa.published = 1 AND dpa.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) ORDER BY created DESC LIMIT 3

126 (77.009201049805): ( SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.video != '' AND dp.video_source != '' AND dp.cat = 10 AND dp.published = 1 AND dp.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) UNION ( SELECT dpa.id, dpa.name, dpa.title, dpa.video, dpa.video_source, dpa.created FROM jos_deeppockets_archive AS dpa WHERE dpa.video != '' AND dpa.video_source != '' AND dpa.cat = 10 AND dpa.published = 1 AND dpa.type != 'deeppockets_item_link' ORDER BY created DESC LIMIT 3 ) ORDER BY created DESC LIMIT 3

127 (392.19856262207): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294800513 LIMIT 1

128 (46.968460083008): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294800513 LIMIT 1

129 (288.00964355469): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294800359 LIMIT 1

130 (42.200088500977): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294800359 LIMIT 1

131 (195.98007202148): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294800361 LIMIT 1

132 (34.093856811523): SELECT dp.id, dp.name, dp.title, dp.video, dp.video_source, dp.created FROM jos_deeppockets AS dp WHERE dp.id = 294800361 LIMIT 1

133 (480.89027404785): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

134 (365.01884460449): SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

135 (277.99606323242): SELECT name FROM jos_deeppockets WHERE id=215

136 (36.001205444336): SELECT name FROM jos_deeppockets WHERE id=215

137 (434.87548828125): SELECT *, DATE_FORMAT(publish_up,'%d %b %Y') AS date_publish_up, DATE_FORMAT(publish_down,'%d %b %Y') AS date_publish_down FROM jos_events WHERE state=1 AND publish_up > NOW() and extra_info REGEXP '((;)|(^))215((;)|($))' AND catid IN (0,110) ORDER BY publish_up ASC LIMIT 3

138 (398.15902709961): SELECT *, DATE_FORMAT(publish_up,'%d %b %Y') AS date_publish_up, DATE_FORMAT(publish_down,'%d %b %Y') AS date_publish_down FROM jos_events WHERE state=1 AND publish_up > NOW() and extra_info REGEXP '((;)|(^))215((;)|($))' AND catid IN (0,110) ORDER BY publish_up ASC LIMIT 3

139 (61.988830566406): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

140 (47.206878662109): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

141 (!!!!! 9250.8792877197): TRUNCATE TABLE jos_trademed_module

142 (97.990036010742): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.cat=10 AND dp.id=294780321 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

143 (55.074691772461): SELECT dp.*, ch.title as channel, exp.name as author_name, exp.specialization as author_specialization, exp.images as author_photo FROM jos_deeppockets_archive as dp LEFT JOIN jos_experts as exp ON exp.id = dp.author LEFT JOIN jos_deeppockets as ch ON dp.fid = ch.id WHERE 1=1 AND dp.cat=10 AND dp.id=294780321 AND (dp.type='deeppockets_item' OR dp.type='deeppockets_item_link') AND dp.published='1' LIMIT 1

144 (872.13516235352): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

145 (52.928924560547): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND (type='deeppockets_item' OR type='deeppockets_item_link') AND published='1' LIMIT 1

146 (78.916549682617): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

147 (48.160552978516): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

148 (!!!!! 1078.8440704346): SELECT jos_item.* FROM jos_item INNER JOIN jos_number ON jos_item.numberID=jos_number.id WHERE 1=1 AND (jos_item.imgMini<>'') AND jos_item.type='L' AND jos_item.numberID= ( SELECT jos_number.id FROM jos_number WHERE jos_number.journalID IN (10) and jos_number.id in (select distinct jos_number.id from jos_number join jos_item on jos_item.numberid=jos_number.id where jos_item.type='P') ORDER BY (CONVERT(SUBSTRING(issue,1,2),SIGNED) + (CONVERT(SUBSTRING(issue,3,2),SIGNED)*100)) DESC LIMIT 0,1 ) ORDER BY RAND() DESC LIMIT 6

149 (56.982040405273): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

150 (53.167343139648): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

151 (42.915344238281): SELECT fid FROM jos_deeppockets WHERE cat=10 AND id=294780321 AND type='deeppockets_item' AND published='1' union SELECT fid FROM jos_deeppockets_archive WHERE cat=10 AND id=294780321 AND type='deeppockets_item' AND published='1' LIMIT 1

152 (415.08674621582): select distinct links.* from jos_textlinks links join jos_textlinks_placement placement on links.id=placement.link_id where journal_id=(10) and (channel_id=215 or channel_id is null)

153 (38.14697265625): select distinct links.* from jos_textlinks links join jos_textlinks_placement placement on links.id=placement.link_id where journal_id=(10) and (channel_id=215 or channel_id is null)

154 (31.948089599609): SELECT livesite FROM jos_dp_categories WHERE id=10 AND published='1' LIMIT 1

155 (63.896179199219): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

156 (43.153762817383): SELECT * FROM jos_deeppockets WHERE 1=1 AND id=294780321 AND published='1' union SELECT * FROM jos_deeppockets_archive WHERE 1=1 AND id=294780321 AND published='1' LIMIT 1

157 (146.86584472656): select jos_twitters.link from jos_twitters where cat=10

158 (31.948089599609): select jos_facebook.link from jos_facebook where cat=10

159 (29.087066650391): select jos_google_plus.link from jos_google_plus where cat=10

160 (26.941299438477): select jos_linkedin.link from jos_linkedin where cat=10

161 (321.1498260498): update jos_bannersmanager_banner set impmade=impmade+1 where id in(14615,14202,14203)

162 (!!!!! 1682.9967498779): insert into jos_banners_delta values (14615,'2025-06-17 00:23:11','216.73.216.120','view'),(14202,'2025-06-17 00:23:11','216.73.216.120','view'),(14203,'2025-06-17 00:23:11','216.73.216.120','view')

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