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4a:T11fa,Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging. 1. Abstract This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly. 2. Introduction Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With Hypotheses H1 . Can ML algorithms determine cell responses before human intervention is required. H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists. 3. Methods Participants/Sample The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination. Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot. Materials and Procedures Cell culture. Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded. Plate setup. Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. Plates wells use a breathable sealing film and sit in a closed secondary container in the incubator; they are autoclaved after the final image. ( Or left to continue growing until a failure mode occurs to increase the amount of cellular data.) Imaging. All images are taken on an inverted phase-contrast microscope. Exposure, gain and light intensity will be fixed. No plate will spend more than 10 minutes out of the incubator per session. The time out of the incubator will be logged. All images will be taken with the microscopy fields and 5 images will be taken per well. End-point measurements. At 96 h, the plate is photographed against a color reference card to record medium color. Every well is then harvested with its floating cells and counted with trypan blue on a hemocytometer, in duplicate. Annotations for the dataset. Every image will be listed with the experiment and plate, condition, time, passage. Planned Analyses In our experimental pipeline analysis the raw images will be provided archived and unchanged. Two Algorithms will be built and compared. One will consist of an anomaly detector, learning the cells growth curve and spread of the features. Ethics and Data Management This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals. Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive. 5. Budget Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data. 6. References List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript).4b:T1220,Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging. 1. Abstract This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly. 2. Introduction Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With Hypotheses H1 . Can ML algorithms determine cell responses before human intervention is required. H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists. 3. Methods Participants/Sample The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination. Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot. Materials and Procedures Cell culture. Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded. Plate setup. Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. Plates wells use a breathable sealing film and sit in a closed secondary container in the incubator; they are autoclaved after the final image. ( Or left to continue growing until a failure mode occurs to increase the amount of cellular data.) Imaging. All images are taken on an inverted phase-contrast microscope. Exposure, gain and light intensity will be fixed. No plate will spend more than 10 minutes out of the incubator per session. The time out of the incubator will be logged. All images will be taken with the microscopy fields and 5 images will be taken per well. End-point measurements. At 96 h, the plate is photographed against a color reference card to record medium color. Every well is then harvested with its floating cells and counted with trypan blue on a hemocytometer, in duplicate. Annotations for the dataset. Every image will be listed with the experiment and plate, condition, time, passage. Planned Analyses In our experimental pipeline analysis the raw images will be provided archived and unchanged. Two Algorithms will be built and compared. One will consist of an anomaly detector, learning the cells growth curve and spread of the features. Ethics and Data Management This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals. Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive. 5. Budget Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data. 6. References List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript).4c:T22f9,{"type":"doc","content":[{"type":"heading","attrs":{"id":"22925bb2-8f35-4a4d-9f7a-32798463bbad","data-toc-id":"22925bb2-8f35-4a4d-9f7a-32798463bbad","textAlign":"left","level":1},"content":[{"type":"text","text":"Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging. "}]},{"type":"heading","attrs":{"id":"102280b4-4c98-45b4-9bc3-29b415268885","data-toc-id":"102280b4-4c98-45b4-9bc3-29b415268885","textAlign":"left","level":1},"content":[{"type":"text","text":"1. Abstract"}]},{"type":"paragraph","attrs":{"id":"3e85ceae-55f1-43db-b440-a80df2f693e9","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","text":"This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly. "}]},{"type":"heading","attrs":{"id":"a75a40d2-a3e5-458a-9094-1a137760f013","data-toc-id":"a75a40d2-a3e5-458a-9094-1a137760f013","textAlign":null,"level":1},"content":[{"type":"text","text":"2. Introduction"}]},{"type":"paragraph","attrs":{"id":"eab0601e-2596-41b2-958d-227927f52356","class":null,"textAlign":"left"},"content":[{"type":"text","text":"Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With "}]},{"type":"heading","attrs":{"id":"1504af7b-fd4b-47b2-96fe-7947c6b08e82","data-toc-id":"1504af7b-fd4b-47b2-96fe-7947c6b08e82","textAlign":"left","level":3},"content":[{"type":"text","text":"Hypotheses"}]},{"type":"paragraph","attrs":{"id":"69cbe293-7114-4615-8090-415936addfbe","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","text":"H1 . Can ML algorithms determine cell responses before human intervention is required. "}]},{"type":"paragraph","attrs":{"id":"f13d3a01-e378-4b8b-b2b1-1c4a831b8751","class":null,"textAlign":"left"},"content":[{"type":"text","text":"H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists."}]},{"type":"heading","attrs":{"id":"5db21052-1080-4fc0-bce1-4b1a0690b84d","data-toc-id":"5db21052-1080-4fc0-bce1-4b1a0690b84d","textAlign":"left","level":2},"content":[{"type":"text","text":"3. Methods"}]},{"type":"heading","attrs":{"id":"39c552e4-4ee6-4f4f-a880-2b998198760a","data-toc-id":"39c552e4-4ee6-4f4f-a880-2b998198760a","textAlign":"left","level":3},"content":[{"type":"text","text":"Participants/Sample"}]},{"type":"paragraph","attrs":{"id":"e290afab-d7f3-4378-85a5-d382071a1f9a","class":null,"textAlign":"justify"},"content":[{"type":"hardBreak"},{"type":"text","text":"The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination. "},{"type":"hardBreak"},{"type":"text","text":"Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot. "}]},{"type":"heading","attrs":{"id":"62b8f3d6-c707-4b23-8272-1826e8d107db","data-toc-id":"62b8f3d6-c707-4b23-8272-1826e8d107db","textAlign":"left","level":3},"content":[{"type":"text","text":"Materials and Procedures"}]},{"type":"paragraph","attrs":{"id":"8a47998c-8c8b-41e4-8d46-af85adfa9109","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","marks":[{"type":"bold"}],"text":"Cell culture."},{"type":"text","text":" Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded."},{"type":"hardBreak"},{"type":"text","marks":[{"type":"bold"}],"text":"Plate setup."},{"type":"text","text":" Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. Plates wells use a breathable sealing film and sit in a closed secondary container in the incubator; they are autoclaved after the final image. ( Or left to continue growing until a failure mode occurs to increase the amount of cellular data.)"},{"type":"hardBreak"},{"type":"text","marks":[{"type":"bold"}],"text":"Imaging."},{"type":"text","text":" All images are taken on an inverted phase-contrast microscope. Exposure, gain and light intensity will be fixed. No plate will spend more than 10 minutes out of the incubator per session. The time out of the incubator will be logged. All images will be taken with the microscopy fields and 5 images will be taken per well."}]},{"type":"paragraph","attrs":{"id":"f028706d-fc57-49f0-b5aa-bc84e2308233","class":null,"textAlign":"left"},"content":[{"type":"text","marks":[{"type":"bold"}],"text":"End-point measurements."},{"type":"text","text":" At 96 h, the plate is photographed against a color reference card to record medium color. Every well is then harvested with its floating cells and counted with trypan blue on a hemocytometer, in duplicate."},{"type":"hardBreak"},{"type":"text","marks":[{"type":"bold"}],"text":"Annotations for the dataset. "},{"type":"text","text":"Every image will be listed with the experiment and plate, condition, time, passage. "},{"type":"hardBreak"}]},{"type":"heading","attrs":{"id":"5441ad88-0fa0-4c6d-94a3-63a810a56bbd","data-toc-id":"5441ad88-0fa0-4c6d-94a3-63a810a56bbd","textAlign":"left","level":3},"content":[{"type":"text","text":"Planned Analyses"}]},{"type":"paragraph","attrs":{"id":"a8174e24-da95-4fd2-8514-a83f2773a60d","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","text":"In our experimental pipeline analysis the raw images will be provided archived and unchanged. Two Algorithms will be built and compared. One will consist of an anomaly detector, learning the cells growth curve and spread of the features. "}]},{"type":"heading","attrs":{"id":"16fe8d55-579c-442d-b1fe-4daddd0cdabc","data-toc-id":"16fe8d55-579c-442d-b1fe-4daddd0cdabc","textAlign":"left","level":3},"content":[{"type":"text","text":"Ethics and Data Management"}]},{"type":"paragraph","attrs":{"id":"90a7cdea-14b2-4857-8704-e5e32d43dae3","class":null,"textAlign":"left"},"content":[{"type":"text","text":"This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals. "},{"type":"hardBreak"},{"type":"text","text":"Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive. "}]},{"type":"heading","attrs":{"id":"e32a1c94-5782-4da9-afe1-315a939fe81e","data-toc-id":"e32a1c94-5782-4da9-afe1-315a939fe81e","textAlign":"left","level":2},"content":[{"type":"text","text":"5. Budget"}]},{"type":"paragraph","attrs":{"id":"c835f7ed-c2d5-4a48-b857-e951a9188aac","class":null,"textAlign":"left"},"content":[{"type":"text","text":"Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data."}]},{"type":"heading","attrs":{"id":"d9c90060-9401-49ae-af24-d2ec4c002f31","data-toc-id":"d9c90060-9401-49ae-af24-d2ec4c002f31","textAlign":"left","level":2},"content":[{"type":"text","text":"6. References"}]},{"type":"paragraph","attrs":{"id":"21c387e9-720d-45f2-92f0-fd75d7d84e0b","class":null,"textAlign":"left"},"content":[{"type":"text","text":"List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript)."}]}]}4d:T1220,Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging. 1. Abstract This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly. 2. Introduction Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With Hypotheses H1 . Can ML algorithms determine cell responses before human intervention is required. H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists. 3. Methods Participants/Sample The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination. Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot. Materials and Procedures Cell culture. Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded. Plate setup. Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. Plates wells use a breathable sealing film and sit in a closed secondary container in the incubator; they are autoclaved after the final image. ( Or left to continue growing until a failure mode occurs to increase the amount of cellular data.) Imaging. All images are taken on an inverted phase-contrast microscope. Exposure, gain and light intensity will be fixed. No plate will spend more than 10 minutes out of the incubator per session. The time out of the incubator will be logged. All images will be taken with the microscopy fields and 5 images will be taken per well. End-point measurements. At 96 h, the plate is photographed against a color reference card to record medium color. Every well is then harvested with its floating cells and counted with trypan blue on a hemocytometer, in duplicate. Annotations for the dataset. Every image will be listed with the experiment and plate, condition, time, passage. Planned Analyses In our experimental pipeline analysis the raw images will be provided archived and unchanged. Two Algorithms will be built and compared. One will consist of an anomaly detector, learning the cells growth curve and spread of the features. Ethics and Data Management This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals. Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive. 5. Budget Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data. 6. References List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript).4e:T22f9,{"type":"doc","content":[{"type":"heading","attrs":{"id":"22925bb2-8f35-4a4d-9f7a-32798463bbad","data-toc-id":"22925bb2-8f35-4a4d-9f7a-32798463bbad","textAlign":"left","level":1},"content":[{"type":"text","text":"Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging. "}]},{"type":"heading","attrs":{"id":"102280b4-4c98-45b4-9bc3-29b415268885","data-toc-id":"102280b4-4c98-45b4-9bc3-29b415268885","textAlign":"left","level":1},"content":[{"type":"text","text":"1. Abstract"}]},{"type":"paragraph","attrs":{"id":"3e85ceae-55f1-43db-b440-a80df2f693e9","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","text":"This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly. "}]},{"type":"heading","attrs":{"id":"a75a40d2-a3e5-458a-9094-1a137760f013","data-toc-id":"a75a40d2-a3e5-458a-9094-1a137760f013","textAlign":null,"level":1},"content":[{"type":"text","text":"2. Introduction"}]},{"type":"paragraph","attrs":{"id":"eab0601e-2596-41b2-958d-227927f52356","class":null,"textAlign":"left"},"content":[{"type":"text","text":"Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With "}]},{"type":"heading","attrs":{"id":"1504af7b-fd4b-47b2-96fe-7947c6b08e82","data-toc-id":"1504af7b-fd4b-47b2-96fe-7947c6b08e82","textAlign":"left","level":3},"content":[{"type":"text","text":"Hypotheses"}]},{"type":"paragraph","attrs":{"id":"69cbe293-7114-4615-8090-415936addfbe","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","text":"H1 . Can ML algorithms determine cell responses before human intervention is required. "}]},{"type":"paragraph","attrs":{"id":"f13d3a01-e378-4b8b-b2b1-1c4a831b8751","class":null,"textAlign":"left"},"content":[{"type":"text","text":"H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists."}]},{"type":"heading","attrs":{"id":"5db21052-1080-4fc0-bce1-4b1a0690b84d","data-toc-id":"5db21052-1080-4fc0-bce1-4b1a0690b84d","textAlign":"left","level":2},"content":[{"type":"text","text":"3. Methods"}]},{"type":"heading","attrs":{"id":"39c552e4-4ee6-4f4f-a880-2b998198760a","data-toc-id":"39c552e4-4ee6-4f4f-a880-2b998198760a","textAlign":"left","level":3},"content":[{"type":"text","text":"Participants/Sample"}]},{"type":"paragraph","attrs":{"id":"e290afab-d7f3-4378-85a5-d382071a1f9a","class":null,"textAlign":"justify"},"content":[{"type":"hardBreak"},{"type":"text","text":"The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination. "},{"type":"hardBreak"},{"type":"text","text":"Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot. "}]},{"type":"heading","attrs":{"id":"62b8f3d6-c707-4b23-8272-1826e8d107db","data-toc-id":"62b8f3d6-c707-4b23-8272-1826e8d107db","textAlign":"left","level":3},"content":[{"type":"text","text":"Materials and Procedures"}]},{"type":"paragraph","attrs":{"id":"8a47998c-8c8b-41e4-8d46-af85adfa9109","class":null,"textAlign":"left"},"content":[{"type":"hardBreak"},{"type":"text","marks":[{"type":"bold"}],"text":"Cell culture."},{"type":"text","text":" Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded."},{"type":"hardBreak"},{"type":"text","marks":[{"type":"bold"}],"text":"Plate setup."},{"type":"text","text":" Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. 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"}]},{"type":"heading","attrs":{"id":"16fe8d55-579c-442d-b1fe-4daddd0cdabc","data-toc-id":"16fe8d55-579c-442d-b1fe-4daddd0cdabc","textAlign":"left","level":3},"content":[{"type":"text","text":"Ethics and Data Management"}]},{"type":"paragraph","attrs":{"id":"90a7cdea-14b2-4857-8704-e5e32d43dae3","class":null,"textAlign":"left"},"content":[{"type":"text","text":"This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals. "},{"type":"hardBreak"},{"type":"text","text":"Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive. "}]},{"type":"heading","attrs":{"id":"e32a1c94-5782-4da9-afe1-315a939fe81e","data-toc-id":"e32a1c94-5782-4da9-afe1-315a939fe81e","textAlign":"left","level":2},"content":[{"type":"text","text":"5. Budget"}]},{"type":"paragraph","attrs":{"id":"c835f7ed-c2d5-4a48-b857-e951a9188aac","class":null,"textAlign":"left"},"content":[{"type":"text","text":"Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data."}]},{"type":"heading","attrs":{"id":"d9c90060-9401-49ae-af24-d2ec4c002f31","data-toc-id":"d9c90060-9401-49ae-af24-d2ec4c002f31","textAlign":"left","level":2},"content":[{"type":"text","text":"6. References"}]},{"type":"paragraph","attrs":{"id":"21c387e9-720d-45f2-92f0-fd75d7d84e0b","class":null,"textAlign":"left"},"content":[{"type":"text","text":"List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript)."}]}]}4f:T1d4a,

Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging.

1. Abstract

This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly.

2. Introduction

Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With

Hypotheses

H1 . Can ML algorithms determine cell responses before human intervention is required.

H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists.

3. Methods

Participants/Sample

The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination.
Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot.

Materials and Procedures

Cell culture. Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded.
Plate setup. Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. Plates wells use a breathable sealing film and sit in a closed secondary container in the incubator; they are autoclaved after the final image. ( Or left to continue growing until a failure mode occurs to increase the amount of cellular data.)
Imaging. All images are taken on an inverted phase-contrast microscope. Exposure, gain and light intensity will be fixed. No plate will spend more than 10 minutes out of the incubator per session. The time out of the incubator will be logged. All images will be taken with the microscopy fields and 5 images will be taken per well.

End-point measurements. At 96 h, the plate is photographed against a color reference card to record medium color. Every well is then harvested with its floating cells and counted with trypan blue on a hemocytometer, in duplicate.
Annotations for the dataset. Every image will be listed with the experiment and plate, condition, time, passage.

Planned Analyses

In our experimental pipeline analysis the raw images will be provided archived and unchanged. Two Algorithms will be built and compared. One will consist of an anomaly detector, learning the cells growth curve and spread of the features.

Ethics and Data Management

This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals.
Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive.

5. Budget

Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data.

6. References

List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript).

50:T1d4a,

Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging.

1. Abstract

2. Introduction

Hypotheses

H1 . Can ML algorithms determine cell responses before human intervention is required.

H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists.

3. Methods

Participants/Sample

Materials and Procedures

Planned Analyses

Ethics and Data Management

5. Budget

Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data.

6. References

List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript).

51:T1220,Early Automated Detection of Cell Culture Failure from Time-Lapse Imaging. 1. Abstract This study will consists of an incubated mammalian cell type over their weekly growth period. The purpose of the study is to determine whether ML models can determine whether cell growth will fail or succeed in a rapid timeline. The work will be carried out by Andre Childs (PI) at the Dallas Maker Space’s cell culture laboratory. The duration of the project will be last 12 weeks from funding to delivery. Raw images with annotations, protocols and processing logs will be licensed to the CUI Fund Pilot under written agreement and archived openly. 2. Introduction Cell cultures fail through overgrowth, poor attachment, contamination and environmental and media changes. These failure are currently found after inspection from human intervention days after a culture begins or when media changes are required. [1] This is a large loss to studies as it wastes cultured cells, media, consumable but most of all the scientists time as weekends are often required to inspect cells at both the academic and industrial level. With Hypotheses H1 . Can ML algorithms determine cell responses before human intervention is required. H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists. 3. Methods Participants/Sample The target sample will be HEK293 Mammalian cells. Cell growth wells contaminated, failed and successful will provided. Cell lines will be purchased from the ATTC and studied in within 4 different independent experiments seeded on different days. The experiment will consist of 1. Healthy seeded at recommended density given the low doses of nutrients. 2. Healthy cells seeded at the recommended density and the proper amount of nutrients. 3. Healthy Cells given higher doses of nutrients. 4. Healthy cells seeded at the recommended density and proper amount of nutrients spiked with microbial contamination. Temperatures will remain consistent throughout each of the different experimental procedures. lmaging will occur with a bottom up microscope at given times of 1,2,3, 5 and 7 days. Incubator lapse image videos will also be provided to the licensed CUI Fund Pilot. Materials and Procedures Cell culture. Cells grow in DMEM (high glucose) with 10% fetal bovine serum at 37 °C and 5% CO2 and are passaged at 70–90% confluence with trypsin-EDTA. Antibiotics are omitted from one passage before seeding onward, so that contamination is not masked. Medium and serum lot numbers are recorded. Plate setup. Healthy wells are seeded at different densities as specified in the Sample section density. Condition positions follow a pre-generated randomized layout. Plates wells use a breathable sealing film and sit in a closed secondary container in the incubator; they are autoclaved after the final image. ( Or left to continue growing until a failure mode occurs to increase the amount of cellular data.) Imaging. All images are taken on an inverted phase-contrast microscope. Exposure, gain and light intensity will be fixed. No plate will spend more than 10 minutes out of the incubator per session. The time out of the incubator will be logged. All images will be taken with the microscopy fields and 5 images will be taken per well. End-point measurements. At 96 h, the plate is photographed against a color reference card to record medium color. Every well is then harvested with its floating cells and counted with trypan blue on a hemocytometer, in duplicate. Annotations for the dataset. Every image will be listed with the experiment and plate, condition, time, passage. Planned Analyses In our experimental pipeline analysis the raw images will be provided archived and unchanged. Two Algorithms will be built and compared. One will consist of an anomaly detector, learning the cells growth curve and spread of the features. Ethics and Data Management This study uses an established and commercially available distributed human cell line and involved no patients, patient identifiable data or animals. Data management will consist of seperate raw images, kept under lock and key. Admin privileges are only allowed to view the working drive. 5. Budget Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data. 6. 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Hypotheses

H1 . Can ML algorithms determine cell responses before human intervention is required.

H2. Can a model trained from the first 24 hours predict which well have failed before 96 hours have passed or become visible to assay developmental scientists.

3. Methods

Participants/Sample

Materials and Procedures

Planned Analyses

Ethics and Data Management

5. Budget

Provide an itemized list of anticipated costs (materials, personnel, etc.). These are not binding and are able to be adjusted based on the results of the pilot data.

6. References

List all references used in the manuscript using Nature style (e.g. numbered in-text citations and alphabetical references at the end of the manuscript).

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