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Backed by cutting edge technology, an uncompromising focus on ease-of-use and dedicated customer service, Indica Labs’ software and services are being used to make vital discoveries in pathology labs and research organizations around the world.

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Press Release: Indica Labs and Hamamatsu Photonics K.K. Announce Collaboration to Provide Optimized Integrated Digital Pathology Workflows

Albuquerque, NM and Hamamatsu City, Japan, - 14th October 2022 - Indica Labs, an industry leader in quantitative digital pathology and image management solutions, and Hamamatsu Photonics K.K., a forerunner in whole slide imaging systems, announced an agreement to maintain long-term interoperability between Indica Labs’ HALO AP® software platform and Hamamatsu’s NanoZoomer family of high-speed, high-resolution scanners. ...

Multiplexing Demo Request

REQUEST A LIVE HALO® MULTIPLEXING DEMONSTRATION If you are interested in a live HALO® multiplexing demonstration, submit the form below. Once your form has been submitted one of our talented Applications Scientists will reach out to schedule your demo! [wpforms id="36460" title="false"]...

Proof-of-concept Multiplexing

PROOF-OF-CONCEPT MULTIPLEX IMAGE ANALYSIS See HALO® in action on up to three of your images with a free analysis. Click here to view our supported file formats. /*! elementor - v3.6.3 - 12-04-2022 */.elementor-heading-title{padding:0;margin:0;line-height:1}.elementor-widget-heading .elementor-heading-title[class*=elementor-size-]>a{color:inherit;font-size:inherit;line-height:inherit}.elementor-widget-heading .elementor-heading-title.elementor-size-small{font-size:15px}.elementor-widget-heading .elementor-heading-title.elementor-size-medium{font-size:19px}.elementor-widget-heading .elementor-heading-title.elementor-size-large{font-size:29px}.elementor-widget-heading .elementor-heading-title.elementor-size-xl{font-size:39px}.elementor-widget-heading .elementor-heading-title.elementor-size-xxl{font-size:59px} How it works:   Submit the form below. An Applications Scientist will respond to your request within one business day. They will inquire about your image analysis goals for each image. Upload 1-3 images to a OneDrive folder location provided by the Applications Scientist. ...

Towards Open Pathology: Facilitating Development of Novel AI-based Tools for Digital Pathology through Collaboration and Integration

16 October 2022 | In this 1-hour workshop, Eric Runde, Chief Operating Officer at Indica Labs, will introduce Indica’s platforms, our collaborative approach to incorporating artificial intelligence (AI) into life science and clinical workflows, and the open pathology tools available to developers and industry partners. Dr. Peter Caie, Principal Scientist of AI Collaborations at Indica Labs, will present case studies of customer collaborations resulting in the development and validation of commercially available and inter-operable AI algorithms addressing customer needs....

Press Release: Leica Biosystems Announces Partnership with Indica Labs to Deliver Integrated Digital Pathology Workflow Solutions for Mutual Customers

Vista, CA - Sep 4, 2022, Leica Biosystems, a cancer diagnostics company and a global leader in workflow solutions, and Indica Labs, the industry-leading provider of computational and image management software in digital pathology, today announced a partnership focused on delivering compatible digital pathology workflow solutions. ...

Press Release: Indica Labs Announces Collaboration with The Industrial Centre for Artificial Intelligence Research in Digital Diagnostics (iCAIRD) for the Development of an AI-based Algorithm for the Automated Reporting of Lymph Node Status in Colon Cancer

Albuquerque, NM, and Glasgow, Scotland, – 30 August, 2022 – Indica Labs, an industry leader in quantitative digital pathology and image management solutions, and The Industrial Centre for Artificial Intelligence Research in Digital Diagnostics (iCAIRD), announced today an agreement to collaborate on the development of an AI-based digital pathology solution for the detection of cancer within lymph nodes from colorectal surgery cases....

Press Release: Deep Bio successfully integrates DeepDx® Prostate algorithm into HALO AP® platform from Indica Labs

Seoul, South Korea, and Albuquerque, NM – August 9, 2022 – Deep Bio, a company concentrating on SaMD (Software as a Medical Device) for digital pathology, is offering clinically validated, AI-based DeepDx® algorithms, and Indica Labs, a leading provider of computational pathology software and services, are excited to announce the successful integration of the DeepDx® Prostate algorithm into the HALO AP® platform from Indica Labs. ...

New Microglial Activation modules are now available!

New Microglial Activation modules are now available! Submit the form below to request your upgrade. /*! elementor - v3.6.3 - 12-04-2022 */ .elementor-heading-title{padding:0;margin:0;line-height:1}.elementor-widget-heading .elementor-heading-title[class*=elementor-size-]>a{color:inherit;font-size:inherit;line-height:inherit}.elementor-widget-heading .elementor-heading-title.elementor-size-small{font-size:15px}.elementor-widget-heading .elementor-heading-title.elementor-size-medium{font-size:19px}.elementor-widget-heading .elementor-heading-title.elementor-size-large{font-size:29px}.elementor-widget-heading .elementor-heading-title.elementor-size-xl{font-size:39px}.elementor-widget-heading .elementor-heading-title.elementor-size-xxl{font-size:59px} How it works:   Following submission of an upgrade request form, a member of our Technical Solutions Team will reach out via email to advise you of the earliest available installation appointments for your region and schedule your software upgrade(s) accordingly. [wpforms id="35906" title="false"] Questions? Email support@indicalab.com where your local Applications Scientist and/or Technical Solutions Engineer will be available to answer any...

3.5 Upgrade request

HALO, HALO AI, and HALO Link 3.5 are now available! If you do not have an active SMS plan but would like to upgrade to 3.5, you will need to purchase SMS coverage for your product license(s). You can do so by clicking the button below. Purchase SMS Coverage How it works: If you have an active Software Maintenance and Support (SMS) plan, you can complete the form below to request your upgrade. Following submission of an upgrade request form, a member of our Technical...

Object Colocalization modules 2.1 for BF and FL Upgrade form

Object Colocalization modules 2.1 for BF and FL are now available! Submit the form below to request your upgrade. How it works: Following submission of an upgrade request form, a member of our Technical Solutions Team will reach out via email to advise you of the earliest available installation appointments for your region and schedule your software upgrade(s) accordingly. [wpforms id="35654" title="false"] Questions?Email support@indicalab.com where your local Applications Scientist and/or Technical Solutions Engineer will be available to answer any questions you may have on these releases. Want to learn more about...

HALO AI Demo Request

REQUEST A LIVE HALO AI SOFTWARE DEMONSTRATION If you are interested in a live HALO AI software demonstration, submit the form below. Once your form has been submitted one of our talented Applications Scientists will reach out to schedule your demo! [wpforms id="35428" title="false"]...

Proof-of-concept image analysis with HALO AI™

PROOF-OF-CONCEPT IMAGE ANALYSIS WITH HALO AI™ See HALO AI™ in action on up to three of your images with a free analysis. Click here to view our supported file formats. How it works: Submit the form below. An Applications Scientist will respond to your request within one business day. They will inquire about your image analysis goals for each image. Upload 1-3 images to a OneDrive folder location provided by the Applications Scientist. Arrange a virtual meeting to discuss your image analysis results with an...

Press Release: Indica Labs receives top honor in Albuquerque Journal ‘Flying 40’ list of top tech firms in New Mexico

Albuquerque, NM, 13 June, 2022 – Indica Labs, a leading provider of computational pathology software and services is proud to announce today they have received the top award in the Albuquerque Journal ‘Flying 40’ analysis of technology firms in New Mexico. Indica Labs participated in the Flying 40 for the first time in 2022 and received the top honor based on a 323% increase in revenue over the past 5 years. In that same time period, the number of employees...

HALO Link 3.5 Sneak Peek

14 July 2022 | A new version of HALO Link, the collaborative image management platform from Indica Labs is coming soon! In this 1-hour webinar, Kat Latimer of the Product Management team will discuss and demonstrate the new features and functionalities and will end with a Q/A session....

HALO AP 2.0 Upgrade form

HALO AP® 2.0 is now available! Submit the form below to request your upgrade. How it works: Following submission of an upgrade request form, a member of our Technical Solutions Team will reach out via email to advise you of the earliest available installation appointments for your region and schedule your software upgrade(s) accordingly. [wpforms id="35076" title="false"] Questions?Email support@indicalab.com where your local Applications Scientist and/or Technical Solutions Engineer will be available to answer any questions you may have on these releases. Want to learn more about HALO AP 2.0?Check out our...

Press Release: Lunaphore and Indica Labs announce partnership to provide complete technology solution for spatial biology and image analysis

LAUSANNE, Switzerland and ALBUQUERQUE, N.M. – May 12, 2022 – 5 pm (CET) | 9 am MDT – Lunaphore, a Swiss life sciences company developing technology to enable spatial biology in every laboratory, and Indica Labs, a leading provider of computational pathology software and services, today announced a partnership to co-market an end-to-end solution that combines Lunaphore’s flagship COMET™ spatial biology platform and Indica’s HALO® and HALO AI™ digital pathology image analysis software....

HALO AP 2.0 Features and Functionalities

In this blog post, you can learn about the new features in HALO AP 2.0, the CE marked anatomic pathology case management software from Indica Labs, where to find training resources and documentation, and how the upgrade will be rolled out. ...

Interested in Quantitative Image Analysis in Oncology?

In this blog post, you can learn about what the team at Indica Labs has planned for the upcoming AACR 2022 conference in New Orleans! From April 10-13, our team will be in  booth #1147, and our Applications Scientists will be available to answer any questions you have about how our HALO® software suite can advance your oncology research and can provide you with a demonstration of the latest release of our flagship HALO® image analysis software, our powerful HALO AI™ deep learning add-on, and our HALO Link™ collaborative...

Announcing the Vacuole Quantification module v3.2

/*! elementor - v3.5.0 - 12-12-2021 */.elementor-widget-image{text-align:center}.elementor-widget-image a{display:inline-block}.elementor-widget-image a img[src$=".svg"]{width:48px}.elementor-widget-image img{vertical-align:middle;display:inline-block} We’re excited to announce the launch of the updated Vacuole Quantification module v3.2!  In this blog post, you can learn about some of the new features in this module, where to find the user guide and tutorial video, and when to expect to upgrade. /*! elementor - v3.5.0 - 12-12-2021 */.elementor-heading-title{padding:0;margin:0;line-height:1}.elementor-widget-heading .elementor-heading-title[class*=elementor-size-]>a{color:inherit;font-size:inherit;line-height:inherit}.elementor-widget-heading .elementor-heading-title.elementor-size-small{font-size:15px}.elementor-widget-heading .elementor-heading-title.elementor-size-medium{font-size:19px}.elementor-widget-heading .elementor-heading-title.elementor-size-large{font-size:29px}.elementor-widget-heading .elementor-heading-title.elementor-size-xl{font-size:39px}.elementor-widget-heading .elementor-heading-title.elementor-size-xxl{font-size:59px} What New Features are Included in the Module? This major module update includes the following features: ...

Vacuole Module 3.2 Upgrade form

Vacuole Module 3.2 is now available! Submit the form below to request your upgrade. How it works: Following submission of an upgrade request form, a member of our Technical Solutions Team will reach out via email to advise you of the earliest available installation appointments for your region and schedule your software upgrade(s) accordingly. [wpforms id="34783" title="false"] Questions?Email support@indicalab.com where your local Applications Scientist and/or Technical Solutions Engineer will be available to answer any questions you may have on these releases. Want to learn more about Vacuole module v3.2?Check out...

HALO AP 2.0 Sneak Peek

29 March 2022 | A new version of HALO AP, Indica Labs’ clinical case management software, is coming soon! HALO AP 2.0 reimagines the pathologist’s cockpit with an updated case viewer and several new workflow enhancements. In this hour-long webinar, we will demonstrate these new features and end with a Q&A session. ...

Optimizing quantitative analysis of highly multiplexed CODEX images in HALO

31 March 2022 | In this webinar, Dr. Noemi Kedei, a staff scientist at the Collaborative Protein Technology Resource core of the Center for Cancer Research (CCR) at the National Cancer Institute, will present a comprehensive CODEX workflow, from image acquisition to image processing and HALO image analysis. Dr. Kedei leads the core facility that provides this technology as service to CCR investigators, including project consultation and design, antibody panel customization, tissue staining and imaging, image processing, and...

Software Maintenance and Support (SMS) Plan Request

Software Maintenance and Support (SMS) Coverage Software Upgrades Newest releases like HALO, HALO AI, and HALO Link 3.5 – which are now being scheduled for install. Plus unlimited access to updates like software patches and bug fixes​ between major releases. Support World class technical and application support from our Technical Solutions Engineers...

3.4 Upgrade request

HALO, HALO AI, and HALO Link 3.4 are now available! If you do not have an active SMS plan but would like to upgrade to 3.4, you will need to purchase SMS coverage for your product license(s). You can do so by clicking the button below. Purchase SMS Coverage How it works: If you have an active Software Maintenance and Support (SMS) plan, you can complete the form below to request your upgrade. Following submission of an upgrade request form, a member of our Technical...

RNAscope common questions, troubleshooting, and tips and tricks

When performing RNAscope image analysis, you can set yourself up for success with a combination of thoughtful experimental design, rigorous assay execution and validation. At Indica Labs, the most common challenges we see in RNAscope image analysis include chromogenic staining that has saturated to black, which causes color deconvolution challenges, loss of nuclear morphology due to over-digestion of tissue, and failing to verify and validate an image analysis solution before scaling up....

Bridge the Gap with Indica Labs’ Pharma Services

At Indica Labs, our Pharma Services team is here to help you extract more data from your biomarker assays with our digital image analysis services. From single biomarker IHC to ISH/FISH and highly multiplexed fluorescence and imaging mass cytometry, we offer quantitative image analysis solutions with our own HALO and HALO AI analysis platforms. With over 150 completed image analysis projects, our team has experience across multiple disease areas, applications, and assay types, including immune phenotyping in tumors, biomarker expression...

Proof-of-concept image analysis

PROOF-OF-CONCEPT IMAGE ANALYSIS See HALO® or HALO AI™ in action on up to three of your images with a free analysis. Click here to view our supported file formats. How it works: Submit the form below. An Applications Scientist will respond to your request within one business day. They will inquire about your image analysis goals for each image. Upload 1-3 images to a OneDrive folder location provided by the Applications Scientist. Arrange a virtual meeting to discuss your image analysis results with an Application...

2021: A Year in Review at Indica Labs

As 2021 draws to a close, the team at Indica Labs would like to take this opportunity to reflect on the year and to thank our customers for their continued support through this second pandemic year. Despite the ongoing challenges that the pandemic presents, we celebrate the achievements of our customers who have published over 250 publications in peer-reviewed journals this year with an impressive average impact factor of 9.12. To learn more about these publications spanning immuno-oncology, oncology, immunology,...

A Deep Learning Convolutional Neural Network Can Differentiate Between Helicobacter Pylori Gastritis and Autoimmune Gastritis with Results Comparable to Gastrointestinal Pathologists

13 January 2022 | In this 60-minute webinar, researchers and pathologists from the University of New Mexico will discuss their recently published study using the HALO AI™ deep learning convolutional neural network (CNN) to determine whether a CNN can differentiate autoimmune gastritis from Helicobacter pylori gastritis....

Adoption of the HALO® Platform at Caris Life Sciences’ High Volume Digital Pathology Laboratory

17 October 2021 | In this one-hour pre-conference workshop, Indica Labs is pleased to host Dr. Matthew Oberley, Executive Medical Director at Caris Life Sciences, who will present a case study on deploying HALO AP® case management software in their high-volume, fully digital, anatomic pathology lab. Dr. Oberley will discuss the challenges and selection criteria that led to the adoption of HALO AP, describe the integration into their laboratory workflows, and, finally, touch on the rollout progress and future plans...

THYROID MALT LYMPHOMA:  SELF-HARM TO GAIN POTENTIAL T-CELL HELP

28 October 2021 | The development of extranodal marginal zone lymphoma of mucosa-associated lymphoid tissue (MALT) is driven by chronic inflammatory responses and acquired genetic changes.  To investigate its genetic bases, we performed targeted sequencing of 93 genes in 131 MALT lymphomas including 76 from the thyroid. We found frequent deleterious mutations of TET2 (86%), CD274 (53%), TNFRSF14 (53%) and TNFAIP3 (30%) in thyroid MALT lymphoma....

HALO AP 1.3 Sneak Peek

14 October 2021 | The next release of HALO AP®, Indica Labs' state of the art anatomic pathology software, will be available soon. Join us to see all the new features focused on simplifying the transition to digital case review and hear about our recent CE Mark award for use in primary diagnosis. As anatomic pathology labs transition to digital, it's important that their image management software simplifies case review, is compatible with a wide range of scanners and...

Automated detection and quantitation of gastric immune cells in a mouse model of Helicobacter pylori­-driven preneoplastic progression

21 October 2021 | Gastric cancer is the fourth-leading cause of cancer death worldwide. About 80% of cases are attributable to infection with the bacterium Helicobacter pylori (Hp). Untreated Hp infection causes lifelong stomach inflammation that does not eradicate the bacterium. In some individuals, stomach inflammation leads to preneoplastic progression, a series of sequential tissue changes including loss of gastric acid-producing parietal cells, metaplasia, dysplasia, and finally cancer....

CD38 in the Prostate Tumor Microenvironment

6 October 2021 | CD38, a druggable ectoenzyme, is involved in the generation of adenosine, which is implicated in tumor immune evasion. Its expression and role in prostate tumor-infiltrating immune cells (TIICs) have not been elucidated. We characterized CD38 expression on prostate cancer (PC) epithelial cells and TIICs and explored the association of this expression with clinical outcomes. RNAseq from 159 patients with metastatic castration-resistant prostate cancer (mCRPC) in the International Stand Up To Cancer/Prostate Cancer Foundation (SU2C/PCF) cohort and 171...

Press Release: Indica Labs earns Work/Life Flexibility award and is named a Top Workplace by The Albuquerque Journal for the second year running

Albuquerque, NM, 2 September, 2021 – Indica Labs, a leading provider of computational pathology software, is proud to announce that they have been awarded a Top Workplaces™ honor by The Albuquerque Journal for a second year in a row.  In addition to being a Top Workplace, Indica Labs was the sole recipient of the Life/Work Flexibility award for 2021....

An interview with Charles Habermehl, Software Engineer (Previous Intern)

Q1. As an intern, what projects were you assigned to work on? What skills did you acquire or improve while working on these projects? A1. As an intern I was assigned to work on the Halo Link team. Before working on the Halo Link team I had no experience in Web Development which is the main skill I picked up in my time here so far. To be specific, before I started I did not know JavaScript and am now quite...

An interview with Anas Gauba, Software Engineer (Previous Intern)

Q1. As an intern, what projects were you assigned to work on? What skills did you acquire or improve while working on these projects? A1. As an intern, I worked on the project to build quota-system where the customer can buy some quota whether it be quota for doing analysis, disk storage, etc. I also worked on building a loginAttempt feature where we can track important information such as customers’ ip address and which service they logged in from. The projects...

An interview with Dylan Balata, Software Engineer (Previous Intern)

Q1. As an intern, what projects were you assigned to work on? What skills did you acquire or improve while working on these projects? A1. As an intern I worked on developing ASP.NET Core based infrastructure solutions utilizing https/web socket technology while incorporating native and db interactions. Q2. What do you enjoy most about working at Indica Labs?...

Automated Detection and Gleason Grading of Prostate Cancer in Digital Pathology

8 September 2021 | Digital pathology provides an advantage of automatizing many routine pathological tasks via computational algorithms and tools. The reporting of prostate cases is time-consuming due to a large number of slides per case. Moreover, tumor aggressivity grading (Gleason score) is well known for its subjective nature and high levels of interobserver variability. In this webinar, we will demonstrate a deep learning-based tool developed for the detection of prostate cancer in histological slides (prostate biopsies and prostatectomy...

Press Release: Nottingham University Hospitals NHS Trust selects Indica Labs to deliver their Digital Pathology Solution with HALO AP

Albuquerque, NM, USA and Nottingham, UK, 1 July, 2021 – Following a formal tender process, Nottingham University Hospitals (NUH) NHS Trust today announced the selection of Indica Labs to aid in full digitisation of the pathology workflow. Indica Labs will deliver its leading digital pathology software, HALO AP®, fully integrated with existing hospital systems, alongside multiple Hamamatsu Nanozoomer scanners....

Press Release: Indica Labs and Ibex Partner to Deliver AI-powered Clinical Workflows for Digital Pathology

ALBUQUERQUE, NM and TEL AVIV, Israel – May 20, 2021 – Indica Labs, an industry leader in quantitative digital pathology & image management solutions, and Ibex Medical Analytics, a pioneer in artificial intelligence (AI) based cancer diagnostics, announced an agreement to integrate the Galen™ AI-based cancer diagnostics platform into the HALO AP® digital pathology workflow platform....

Automated detection and classification of prognostic histopathological features in colorectal cancer using deep learning

9 June 2021 | Deep learning can be applied to both clinical and research based digital pathology. Doing so can bring multiple advantages to both fields. In this talk, Dr. Peter Caie and Dr. Ines Nearchou we will discuss these advantages and describe a specific proof of principle that applies AI to the quantification of an important histopathological feature in colorectal cancer, desmoplastic reaction (DR)....

Approaches to Analyzing Skin Tissue using HALO and HALO AI

6 May 2021 | Application Scientist, Natasha Carmell, will discuss and demonstrate workflow approaches for analysing skin sections stained with H&E and immunofluorescence. Using HALO AI we will identify and segment the corneal layer, epidermis, dermis, cartilage, sebaceous glands and lesions in H&E murine auricular tissues, followed by the segmentation of carcinoma from melanoma in fluorescent multiplexed Melanoma tissue. This AI based tissue segmentation will then be combined with biomarker quantification to identify CD8, CD68 and PDL1 positive populations using...

Tips & Tricks: Batch Processing Productivity Tools

29 April 2021 | Batch processing workflows can be a significant time saver for HALO image analysis. In this masterclass, US Application Scientist Michael Tomac will cover six different batch process workflows available in HALO, including: - Registration, including batch registration of TMAs - Annotation Editing & Deletion - Analysis - Edit Result Layers - Spatial Analysis from scratch and using saved settings - View Settings - Export Michael will also highlight changes in batch workflows introduced in HALO 3.3, so this is a great opportunity for HALO...

HistoTalks: NSH Podcasts

Check out the latest National Society for Histotechnology HistoHelp podcast with Dave Krull and Adam Smith! In Part 1 of the HistoHelp AI in the Lab podcast, David Krull, the NSH podcast expert and AI advocate, talks to Adam Smith, Director of Life Science Applications at Indica Labs, about approaches to implement and validate AI in the lab. Click the tab below to listen and learn a little bit about how to train AI algorithms! In Part 2 of the HistoHelp AI in...

CRISPR-Cas9 gene editing of hepatitis B virus in chronically infected humanized mice

Daniel Stone,et al, Molecular Therapy Methods & Clinical Development, 2021
Hepatitis B leads to over 850,000 deaths annually due to complications from chronic infection including cirrhosis and hepatocellular carcinoma. While antiviral drugs successfully reduce viral loads in patients, a cure does not yet exist. This study out of the Jerome laboratory at the Fred Hutchinson Cancer Research Center performed in vivo gene editing utilizing a mouse model for chronic HBV infections and demonstrated a proof-of-concept of safe and effective...

Monomeric/dimeric forms of Fgf15/FGF19 show differential activity in hepatocyte proliferation and metabolic function

Courtney M. Williams et al, The FASEB Journal, 2021
Williams and colleagues at Regeneron Pharmaceuticals perform structure/function relationship studies on Fgf15 and FGF19 using site-directed mutagenesis and downstream functional assays in order to understand their distinct functions in a common pathway. Both molecules are therapeutic targets due to involvement in hepatocellular carcinoma and bile acid production. This publication identifies a single cysteine residue is identified that controls dimerization and hepatocyte proliferation. Understanding these molecular pathways may inform future...

Multiomic analysis and immunoprofiling reveal distinct subtypes of human angiosarcoma

Jason Yongsheng Chan,et al, The Journal of Clinical Investigation, 2020
To molecularly characterize the rare and aggressive tumors known as angiosarcomas, Chan et al utilized a combination of transcriptomic immuno-oncology profiling with multiplex immunohistochemistry and immunofluorescence. HALO image analysis software was used for the quantification of PD-L1, CD68, CD8, FOXP3, CD15, and ERG. From these studies, three phenotypes of patients were identified according to etiology, anatomical origin, signaling pathways, and the tumor inflammation signature. These distinct biological phenotypes...

Neuron Publication Cover

PNOCARC Neurons Promote Hyperphagia and Obesity upon High-Fat-Diet Feeding

Alexander Jaisl, et al, Neuron, 2020
To advance the molecular understanding of obesity, Jais and colleagues set out to identify neuronal populations in mice that respond to being fed a calorie dense, highly palatable food. They identified prepronociceptin (PNOC)-expressing neurons in the hypothalamus that are activated upon acute high fat diet feeding and promote overconsumption. In this publication, HALO image analysis software was used for quantification of transgene expression in mouse neuronal tissue. Future studies on PNOC-expressing neurons...

An ex vivo tumor fragment platform to dissect response to PD-1 blockade in cancer

Dr. Paula Voabil and colleagues used a patient derived tumor fragment platform to investigate immune responses immediately following PD-1 blockade. The Tissue Classifier Add-on and the Multiplex IHC module of HALO® were used in this publication to quantify immune biomarkers in the tumor and stroma, contributing to their conclusion that the ability of tumors to respond to PD-1 blockage correlates with the ability of intratumoral immune cells to be reactivated by the blockade....

Neoadjuvant immunotherapy leads to pathological responses in MMR-proficient and MMR-deficient early-stage colon cancers

Myriam Chalabi, et al, Nature Medicine, 2020
Immunotherapy is known to be effective in late-stage, mismatch repair (MMR) deficient colorectal cancers but not in MMR proficient cancer. This study reports the early results from the NICHE clinical trial that is evaluating treatment of early stage, nonmetastatic preoperative colon cancer with a CTLA-4 inhibitor and a PD-1 inhibitor. Chalabi and colleagues report that the treatment was well tolerated and that a major pathological response was seen in 19/20 patients with...

Transmission of tauopathy strains is independent of their isoform composition

Zhuohao He, et al, Nature Communications, 2020
The accumulation of aggregated tao proteins in neurons is a hallmark of several neurodegenerative diseases, including Alzheimer’s disease. A challenge in the study of tauopathies has been the lack of an appropriate model system. He and colleagues demonstrate here a new mouse model for human tauopathies where the expression of tao isoforms is similar to that in human adult brains. The Area Quantification Module of HALO played a key role in the analysis...

Mechanical regulation of glycolysis via cytoskeleton architecture

Jin Suk Park,et al, Nature, 2020
Park and colleagues explored the question of how regulation of glycolysis responds to structural changes in tissue architecture and chose lung cells and tissue for their studies due to the regular mechanical stress experienced during respiration. In vitro studies demonstrated downregulation of glycolysis following a change in substrate via the degradation of the platelet isoform of the phosphofructokinase (PFKP) enzyme. In vitro studies also showed that oncogenic transformation changed the ability of PFKP...

Association of COVID-19 inflammation with activation of the C5a–C5aR1 axis

Julien Carvelli, et al, Nature, 2020
Researchers aiming to block excessive lung inflammation in COVID-19 patients found upregulated immune checkpoint biomarkers in patients with a range of COVID-19 symptoms (from paucisymptomatic to acute respiratory distress syndrome). In addition, Carvelli et al found increased expression of C5a, an inflammatory mediator, in serum and the C5aR1 receptor on myeloid cells in COVID-19 patients, which are known to initiate inflammatory responses by recruiting neutrophils and monocytes to lungs. An in vitro neutrophil...

Natural killer cells in the human lung tumor microenvironment display immune inhibitory functions

Jules Russick, et al, Journal for ImmunoTherapy of Cancer, 2020
Natural killer (NK) cells are known to have cytotoxic effector functions in tumor immunosurveillance. More recently, evidence of a second potentially inhibitory or regulatory role have emerged. Here, Russick et al compared expression patterns of NK cells inside tumors to nontumoral NK cells to understand their inhibitory functions in the context of the non-small cell lung carcinoma (NSCLC) tumor microenvironment (TME). These studies identified a novel and specific...

Kaiso (ZBTB33) subcellular partitioning functionally links LC3A/B, the tumor microenvironment, and breast cancer survival

Sandeep K Singhal, et al, Communications Biology, 2021
Singhal and colleagues apply quantitative automated image analysis to investigate the role of a transcriptional regulator, Kaiso, in a diverse cohort of breast cancer tumors. Specifically, they utilized the Highplex FL Module with the Tissue Microarray Module of HALO to characterize the tumor microenvironment in breast cancer TMA cores, including pan-cytokeratin, PD-L1, CD8, and CD68. They found that cytoplasmic Kaiso is associated with an immune-suppressed tumor microenvironment and found novel connections between Kaiso...

Intratumoral interleukin-12 mRNA therapy promotes TH1 transformation of the tumor microenvironment

Susannah L Hewitt, et al, Clinical Cancer Research, 2020
In patients with advanced stage lung disease, it is beneficial to evaluate candidacy for immunotherapy without invasive biopsy testing. Lou et al performed a concordance study to evaluate formalin fixed cell blocks compared to lung tumor resections using a PD-L1 22C3 IHC pharmDx™ assay and found strong concordance between pathologists and HALO image analysis software. Future research will focus on clinical validation by assessing the clinical benefit from immunotherapy following PD-L1 immunohistochemistry...

Early-onset impairment of the ubiquitin-proteasome system in dopaminergic neurons caused by α-synuclein

Chris McKinnon, et al, Acta Neuropathologica Communications, 2020
In this study, McKinnon et al identify overexpression of α-synuclein leading to catalytic impairment of the 26S proteosome in defined regions of rat brains. Brain tissue was fixed following α-synuclein overexpression for immunofluorescence studies of dopaminergic neurons which were quantified by the HALO image analysis platform. Future research will focus on characterizing the relationship between proteasome impairment and neurodegeneration....