Okayama University


Okayama University Medical Research Updates (OU-MRU) Vol.96

December 24, 2021

Source: Okayama University (JAPAN), Public Relations Division
For immediate release: 24 December 2021
Okayama University research: Automated cell image analysis

(Okayama, 24 December) Researchers at Okayama University present in Chromosome Research a tool for automatically classifying light-microscopy images of cells as undergoing cell division or not. The tool, based on deep-learning techniques, is highly important for the field of genetics, as chromosomes (the carriers of genetic code) are most easily observed during cell division.

Chromosomes are the parts of cells containing DNA, the carrier of an organism’s genetic information. Chromosome analysis is a cornerstone of genetics, concerned with the study of heredity in organisms. Observing chromosomes is possible with a light microscope, but only during the process of cell division, when chromosome molecules duplicate and condense. It is therefore necessary to capture the dividing cells, which is typically done by looking for the dividing cells with the eyes using a microscope on a slide with mixture of multiple cells on it, and shoot them manually. Although there is a high demand for automated image analysis, applications are still mostly limited to the analysis of human and laboratory-animal cells, and using them often requires advanced computing skills. Now, Associate Professor NAGAKI Kiyotaka from Okayama University and colleagues have developed an analytic tool based on deep-learning algorithms for processing microscopy images of cells, which is especially useful in the context of plants (for which chromosome number and size vary a lot).

The researchers started from the premise that automated cell image analysis should be user-friendly. Existing deep-learning tools typically involve command-line interfaces, requiring users to have certain computing skills that may go beyond the skill set of geneticists (who are usually not trained as data scientists). Therefore, Associate Professor NAGAKI and colleagues decided to develop a graphical user interface (GUI) using Apple’s Create ML application. The latter is a freely available GUI-based developer tool providing a deep-learning framework.

The deep-learning approach requires a ‘training’ set of images with known content: cells that are either in the process of cell division (called mitosis) or not. Images of mitotic cells display chromosomes, the others do not. The algorithm then ‘trains’ itself with this set of images, and develops its own criteria for deciding whether a mitotic cell is displayed or not, which can then be applied for processing the images that actually need to be analyzed.

The scientists performed tests with training sets with different numbers of images of mitotic and non-mitotic cells of different species of plants. Datasets with 120 or more images resulted in accuracy of more than 80% in correctly classifying plant cells as mitotic or non-mitotic. Associate Professor NAGAKI and colleagues also found that using images from many different species improved the classification accuracy, and that the classification also worked for species not occurring in the training sets.

The main limiting factor of the tool is that it does not run on Windows, the world’s most widespread operating system. The researchers point out that this limitation can be overcome by obtaining an inexpensive Mac, and that their system “has the potential to be used as a deep learning sorter that anyone can use because it can easily build models for sorting using all kinds of biological images.”


A chromosome is a complex biomolecule build from DNA (containing an organism’s genetic material) and protein molecules that help to pack and condense the DNA. Chromosomes are located in the cell nuclei. They can only be observed under a light microscope during a particular phase (called the metaphase) of cell division, just after the duplication of a chromosome has happened, when the two chromosome copies are still joined and in their most condensed form.

Although sequences of images of cells can now routinely be recorded by means of a light microscope, analyzing them still is mainly manual, very tedious task. Associate Professor NAGAKI Kiyotaka from Okayama University and colleagues have now developed a user-friendly computer program with a graphical user interface, based on machine-learning techniques, with which an automated classification of images of cells undergoing, or not undergoing, cell division (i.e., displaying chromosomes, is possible.

Kiyotaka Nagaki, Tomoyuki Furuta, Naoki Yamaji, Daichi Kuniyoshi, Megumi Ishihara, Yuji Kishima, Minoru Murata, Atsushi Hoshino and Hirotomo Takatsuka. Effectiveness of Create ML in microscopy image classifications: A simple and inexpensive deep learning pipeline for non-data scientists. Chromosome Research. Published: 14 October 2021.

Correspondence to
Associate Professor NAGAKI Kiyotaka, Ph.D.
Group of Integrated Genomic Breeding, Institute of Plant
Science and Resources, Okayama University, Kurashi-ki,
710-0046, Japan.
E-mail: nagaki(a)rib.okayama-u.ac.jp
For inquiries, please contact us by replacing (a) with the @ mark.

Further information
Okayama University
1-1-1 Tsushima-naka , Kita-ku , Okayama 700-8530, Japan
Public Relations Division
E-mail: www-adm(a) adm.okayama-u.ac.jp
For inquiries, please contact us by replacing (a) with the @ mark.
Website: //www.okayama-u.ac.jp/index_e.html
Okayama Univ. e-Bulletin: //www.okayama-u.ac.jp/user/kouhou/ebulletin/
We love OKAYAMA UNIVERSITY: https://www.youtube.com/watch?v=7cXlttQIk3E
Okayama University Image Movie(2020)
Okayama University supports the Sustainable Development Goals: https://sdgs.okayama-u.ac.jp/en/

The whole volume : OU-MRU (1- )
Vol.1:Innovative non-invasive ‘liquid biopsy’ method to capture circulating tumor cells from blood samples for genetic testing
Vol.2:Ensuring a cool recovery from cardiac arrest
Vol.3:Organ regeneration research leaps forward
Vol.4:Cardiac mechanosensitive integrator
Vol.5:Cell injections get to the heart of congenital defects
Vol.6:Fourth key molecule identified in bone development
Vol.7:Anticancer virus solution provides an alternative to surgery
Vol.8:Light-responsive dye stimulates sight in genetically blind patients
Vol.9:Diabetes drug helps towards immunity against cancer
Vol.10:Enzyme-inhibitors treat drug-resistant epilepsy
Vol.11:Compound-protein combination shows promise for arthritis treatment
Vol.12:Molecular features of the circadian clock system in fruit flies
Vol.13:Peptide directs artificial tissue growth
Vol.14:Simplified boron compound may treat brain tumours
Vol.15:Metamaterial absorbers for infrared inspection technologies
Vol.16:Epigenetics research traces how crickets restore lost limbs
Vol.17:Cell research shows pathway for suppressing hepatitis B virus
Vol.18:Therapeutic protein targets liver disease
Vol.19:Study links signalling protein to osteoarthritis
Vol.20:Lack of enzyme promotes fatty liver disease in thin patients
Vol.21:Combined gene transduction and light therapy targets gastric cancer
Vol.22:Medical supportive device for hemodialysis catheter puncture
Vol.23:Development of low cost oral inactivated vaccines for dysentery
Vol.24:Sticky molecules to tackle obesity and diabetes
Vol.25:Self-administered aroma foot massage may reduce symptoms of anxiety
Vol.26:Protein for preventing heart failure
Vol.27:Keeping cells in shape to fight sepsis
Vol.28:Viral-based therapy for bone cancer
Vol.29:Photoreactive compound allows protein synthesis control with light
Vol.30:Cancer stem cells’ role in tumor growth revealed
Vol.31:Prevention of RNA virus replication
Vol.32:Enzyme target for slowing bladder cancer invasion
Vol.33:Attacking tumors from the inside
Vol.34:Novel mouse model for studying pancreatic cancer
Vol.35:Potential cause of Lafora disease revealed
Vol.36:Overloading of protein localization triggers cellular defects
Vol.37:Protein dosage compensation mechanism unravelled
Vol.38:Bioengineered tooth restoration in a large mammal
Vol.39:Successful test of retinal prosthesis implanted in rats
Vol.40:Antibodies prolong seizure latency in epileptic mice
Vol.41:Inorganic biomaterials for soft-tissue adhesion
Vol.42:Potential drug for treating chronic pain with few side effects
Vol.43:Potential origin of cancer-associated cells revealed
Vol.44:Protection from plant extracts
Vol.45:Link between biological-clock disturbance and brain dysfunction uncovered
Vol.46:New method for suppressing lung cancer oncogene
Vol.47:Candidate genes for eye misalignment identified
Vol.48:Nanotechnology-based approach to cancer virotherapy
Vol.49:Cell membrane as material for bone formation
Vol.50:Iron removal as a potential cancer therapy
Vol.51:Potential of 3D nanoenvironments for experimental cancer
Vol.52:A protein found on the surface of cells plays an integral role in tumor growth and sustenance
Vol.53:Successful implantation and testing of retinal prosthesis in monkey eyes with retinal degeneration
Vol.54:Measuring ion concentration in solutions for clinical and environmental research
Vol.55:Diabetic kidney disease: new biomarkers improve the prediction of the renal prognosis
Vol.56:New device for assisting accurate hemodialysis catheter placement
Vol.57:Possible link between excess chewing muscle activity and dental disease
Vol.58:Insights into mechanisms governing the resistance to the anti-cancer medication cetuximab
Vol.59:Role of commensal flora in periodontal immune response investigated
Vol.60:Role of commensal microbiota in bone remodeling
Vol.61:Mechanical stress affects normal bone development
Vol.62:3D tissue model offers insights into treating pancreatic cancer
Vol.63:Promising biomarker for vascular disease relapse revealed
Vol.64:Inflammation in the brain enhances the side-effects of hypnotic medication
Vol.65:Game changer: How do bacteria play Tag ?
Vol.66:Is too much protein a bad thing?
Vol.67:Technology to rapidly detect cancer markers for cancer diagnosis
Vol.68:Improving the diagnosis of pancreatic cancer
Vol.69:Early gastric cancer endoscopic diagnosis system using artificial intelligence
Vol.70:Prosthetics for Retinal Stimulation
Vol.71:The nervous system can contribute to breast cancer progression
Vol.72:Synthetic compound provides fast screening for potential drugs
Vol.73:Primary intraocular lymphoma does not always spread to the central nervous system
Vol.74:Rising from the ashes—dead brain cells can be regenerated after traumatic injury
Vol.75:More than just daily supplements — herbal medicines can treat stomach disorders
Vol.76:The molecular pathogenesis of muscular dystrophy-associated cardiomyopathy
Vol.77:Green leafy vegetables contain a compound which can fight cancer cells
Vol.78:Disrupting blood supply to tumors as a new strategy to treat oral cancer
Vol.79:Novel blood-based markers to detect Alzheimer’s disease
Vol.80:A novel 3D cell culture model sheds light on the mechanisms driving fibrosis in pancreatic cancer
Vol.81:Innovative method for determining carcinogenicity of chemicals using iPS cells
Vol.82:Making memories — the workings of a neuron revealed
Vol.83:Skipping a beat — a novel method to study heart attacks
Vol.84:Friend to Foe—When Harmless Bacteria Turn Toxic
Vol.85:Promising imaging method for the early detection of dental caries
Vol.86:Plates and belts — a toolkit to prevent accidental falls during invasive vascular proceduresa
Vol.87:Therapeutic potential of stem cells for treating neurodegenerative disease
Vol.88:Nanotechnology for making cancer drugs more accessible to the brain
Vol.89:Studying Parkinson’s disease with face-recognition software
Vol.90:High levels of television exposure affect visual acuity in children
Vol.91:Meeting high demand: Increasing the efficiency of antiviral drug production in bacteria
Vol.92:Numerical modelling to assist the development of a retinal prosthesis
Vol.93:Repurposing cancer drugs: An innovative therapeutic strategy to fight bone cancer
Vol.94:A berry vine found in Asia proves useful in combating lung cancer
Vol.95:A new avenue for detecting cancer in the blood