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PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗

WE-D-9A-04: Improving Multi-Modality Image Registration Using Edge-Based Transformations

Purpose: Multi-modality deformable image registration (DIR) for head and neck (HN) radiotherapy is difficult, particularly when matching computed tomography (CT) scans with magnetic resonance imaging (MRI) scans. We hypothesized that the ‘shared information’ between images of different modalities was to be found in some form of edge-based transformation, and that novel edge-based DIR methods might outperform standard DIR methods. Methods: We propose a novel method that combines gray-scale edge-based morphology and mutual information (MI) in two stages. In the first step, we applied a modification of a previously published mathematical morphology method as an efficient gray scale edge estimator, with denoising function. The results were fed into a MI-based solver (plastimatch). The method was tested on 5 HN patients with pretreatment CT and MR datasets and associated follow-up weekly MR scans. The followup MRs showed significant regression in tumor and normal structure volumes as compared to the pretreatment MRs. The MR images used in this study were obtained using fast spin echo based T2w images with a 1 mm isotropic resolution and FOV matching the CT scan. Results: In all cases, the novel edge-based registration method provided better registration quality than MI-based DIR using the original CT and MRI images. For example, the mismatch in carotid arteries was reduced from 3–5 mm to within 2 mm. The novel edge-based method with different registration regulation parameters did not show any distorted deformations as compared to the non-realistic deformations resulting from MI on the original images. Processing time was 1.3 to 2 times shorter (edge vs. non-edge). In general, we observed quality improvement and significant calculation time reduction with the new method. Conclusion: Transforming images to an ‘edge-space,’ if designed appropriately, greatly increases the speed and accuracy of DIR.

60 APPLIED LIFE SCIENCES↗

A user's guide for the signal processing software for image and speech compression developed in the Communications and Signal Processing Laboratory (CSPL), version 1

A complete documentation of the software developed in the Communication and Signal Processing Laboratory (CSPL) during the period of July 1985 to March 1986 is provided. Utility programs and subroutines that were developed for a user-friendly image and speech processing environment are described. Additional programs for data compression of image and speech type signals are included. Also, programs for the zero-memory and block transform quantization in the presence of channel noise are described. Finally, several routines for simulating the perfromance of image compression algorithms are included.

Kumar, P.↗

Symposium on Machine Processing of Remotely Sensed Data, Purdue University, West Lafayette, Ind., June 29-July 1, 1976, Proceedings

Papers are presented on the applicability of Landsat data to water management and control needs, IBIS, a geographic information system based on digital image processing and image raster datatype, and the Image Data Access Method (IDAM) for the Earth Resources Interactive Processing System. Attention is also given to the Prototype Classification and Mensuration System (PROCAMS) applied to agricultural data, the use of Landsat for water quality monitoring in North Carolina, and the analysis of geophysical remote sensing data using multivariate pattern recognition. The Illinois crop-acreage estimation experiment, the Pacific Northwest Resources Inventory Demonstration, and the effects of spatial misregistration on multispectral recognition are also considered. Individual items are announced in this issue.

Source record↗

Virtual Microscope Views of the Apollo 11 and 12 Lunar Samples

The Apollo virtual microscope is a means of viewing, over the Internet, polished thin sections of every rock in the Apollo lunar sample collections via software, duplicating many of the functions of a petrological microscope, is described. Images from the Apollo 11 and 12 missions may be viewed at: www.virtualmicroscope.org/content/apollo. Introduction: During the six NASA missions to the Moon from 1969-72 a total of 382 kilograms of rocks and soils, often referred to as "the legacy of Apollo", were collected and returned to Earth. A unique collection of polished thin sections (PTSs) was made from over 400 rocks by the Lunar Sample Curatorial Facility at the Johnson Spacecraft Center (JSC), Houston. These materials have been available for loan to approved PIs but of course they can't be simultaneously investigated by several researchers unless they are co-located or the sample is passed back and forward between them by mail/hand carrying which is inefficient and very risky for irreplaceable material. When The Open University (OU), the world's largest Distance Learning Higher Education Establishment found itself facing a comparable problem (how to supply thousands of undergraduate students with an interactive petrological microscope and a personal set of thin sections), it decided to develop a software tool called the Virtual Microscope (VM). As a result it is now able to make the unique and precious collection of Apollo specimens universally available as a resource for concurrent study by anybody in the world's Earth and Planetary Sciences community. Herein, we describe the first steps of a collaborative project between OU and the Johnson Space Center (JSC) Curatorial Facility to record a PTS for every lunar rock, beginning with those collected by the Apollo 11 and 12 missions. Method: Production of a virtual microscope dedicated to a particular theme divides into four main parts - photography, image processing, building and assembly of virtual microscope components, and publication on a website. Two large research quality microscopes are used to collect all the images required for a virtual microscope. The first is part of an integrated package that utilizes Leica PowerMosaic software and a motorised XYZ stage to generate large area mosaics. It includes a fast acquisition camera and depending on the PTS size normally is used to produce seamless mosaic images consisting of 100-500 individual photographs. If the sample is suitable, three mosaics of each sample are recorded - plane polarised light, between crossed polars and reflected light. In order for the VM to be a true petrological microscope it is necessary to recreate the features of a rotating stage and perform observations using filters to produce polarised light. Thus the petrological VM includes the capability of seeing changes in optical properties (pleochroism and birefringence) during rotation allowing mineral identification. The second microscope in the system provides the functions of the rotating stage. To this microscope we have added a robotically controlled motor to acquire seventy-two images (5 degree intervals) in plane polarised light and between crossed polars. To process the images acquired from the two microscopes involves a combination of proprietary software (Photoshop) and our own in-house code. The final stage involves assembling all the components in an HTML5 environment. Pathfinder investigations: We have undertaken a number of pilot studies to demonstrate the efficacy of the petrological microscope with lunar samples. The first was to make available on-line images collected from the Educational Package of Apollo samples provided by NASA to the UK STFC (Science and Technical Facilities Council) for loan as educational material e.g. for schools. The real PTSs of the samples are now no longer sent out to schools removing the risks associated with transport, accidental breakage and eliminating the possibility of loss. The availability of lunar sample VM-related material was further extended to include twenty-eight specimens from all of the Apollo missions. Some of these samples were made more generally available through an ibook entitled "Moon Rocks: an introduction to the Geology of the Moon," free from the Apple Bookstore. Research possibilities: Although the Virtual Microscope was originally conceived as a teaching aid and was later recognised as a means of public outreach and engagement, we now realize that it also has enormous potential as a high level research tool. Following discussions with the JSC Curators we have received Curation and Analysis Planning Team for Extraterrestrial Materials (CAPTEM) permission to embark on a programme of digitizing the entire lunar sample PTS collection for all three of the above purposes. By the time of the 47th Lunar and Planetary Science Conference (LPSC) we will have completed 81 rocks collected during the Apollo 11 and 12 missions and the data, with cross-links to the Lunar Sample Compendium will go live on the Web at the 47th LPSC. The VM images of the Apollo 11 (41 VM images) and 12 (40 VM images) missions can be viewed at: http:/www.virtualmicroscope.org/content/apollo. The lunar sample VM will enable large numbers of skilled/unskilled microscopists (professional and amateur researchers, educators and students, enthusiasts and the simply curious non-scientists) to share the information from a single sample. It will mean that all the PTSs already cut, even historical ones, could be available for new joint investigations or private study. The scientific return from the collection will increase exponentially as a result of further debate and discussion. Simultaneously the VM will remove the need for making unnecessary multiple samplings, avoid consignment of delicate/breakable specimens (all of which are priceless) to insecure mail/courier services and reduce direct labour and indirect costs, travel budgets and unproductive travelling time necessary for co-location of collaborating researchers. For the future we have already recognized further potential for virtual technology. There is nothing that a petrologist likes more than to see the original rock as a hand specimen. It is entirely possible to recreate virtual hand specimens with 3-D hard and software, already developed for viewing fossils, located within the Curatorial Facility, http://curator.jsc.nasa.gov/lunar/lsc/index.cfm.

Gibson, E. K.↗

Scaling deep learning for material imaging with a pseudo 3D model for domain transfer

The recent introduction of deep learning methods for image processing has greatly advanced the characterization of materials using three-dimensional (3D) X-ray imaging techniques. However, deep learning models often have difficulty performing consistently across images owing to unavoidable variations in imaging conditions, which create inconsistencies even for the same material. As a result, networks must frequently be retrained for new datasets, limiting their applicability and generalization. Thus, it is critical to reduce the variations between images to enable a single model to process multiple datasets. Herein, we introduce P3T-Net, a pseudo-3D domain transfer network that transfers diverse 3D images into a uniform domain before processing using deep learning models. Remarkably, P3T-Net enables the reuse of previously trained networks for processing new images and considerably reduces the computational cost of transferring 3D images across domains. These unique capabilities were demonstrated in the following scenarios: (i) image enhancement of fast scans for geological rock and hydrogen fuel cells, (ii) enhancement of images to match the quality of multi-source imaging for lithium-ion batteries, (iii) accurate segmentation of images captured under different conditions, and (iv) tera-scale 3D transfer (10 11 voxels) on a single GPU. Overall, the proposed approach addresses cross-domain inconsistencies across various materials and conditions, thereby enabling more robust and generalizable deep learning solutions for a wide range of material imaging tasks.

25 ENERGY STORAGE↗

Video Guidance Sensor and Time-of-Flight Rangefinder

A proposed video guidance sensor (VGS) would be based mostly on the hardware and software of a prior Advanced VGS (AVGS), with some additions to enable it to function as a time-of-flight rangefinder (in contradistinction to a triangulation or image-processing rangefinder). It would typically be used at distances of the order of 2 or 3 kilometers, where a typical target would appear in a video image as a single blob, making it possible to extract the direction to the target (but not the orientation of the target or the distance to the target) from a video image of light reflected from the target. As described in several previous NASA Tech Briefs articles, an AVGS system is an optoelectronic system that provides guidance for automated docking of two vehicles. In the original application, the two vehicles are spacecraft, but the basic principles of design and operation of the system are applicable to aircraft, robots, objects maneuvered by cranes, or other objects that may be required to be aligned and brought together automatically or under remote control. In a prior AVGS system of the type upon which the now-proposed VGS is largely based, the tracked vehicle is equipped with one or more passive targets that reflect light from one or more continuous-wave laser diode(s) on the tracking vehicle, a video camera on the tracking vehicle acquires images of the targets in the reflected laser light, the video images are digitized, and the image data are processed to obtain the direction to the target. The design concept of the proposed VGS does not call for any memory or processor hardware beyond that already present in the prior AVGS, but does call for some additional hardware and some additional software. It also calls for assignment of some additional tasks to two subsystems that are parts of the prior VGS: a field-programmable gate array (FPGA) that generates timing and control signals, and a digital signal processor (DSP) that processes the digitized video images. The additional timing and control signals generated by the FPGA would cause the VGS to alternate between an imaging (direction-finding) mode and a time-of-flight (range-finding mode) and would govern operation in the range-finding mode.

Bryan, Thomas↗

Study of one- and two-dimensional filtering and deconvolution algorithms for a streaming array computer

The development of vector processing computers of the streaming array architectures has made possible a dramatic decrease in the time required for the solution of problems, i.e., for those algorithms which readily lend themselves to sequential operations on long vectors. There has concurrently been rapid growth in the applications of the techniques generally known as mathematical digital filtering, also called signal analysis, digital signal processing, time series analysis, and digital image processing. The best known applications of these techniques is to seismic data and two-dimensional images, data types consisting of very large collections of numbers. A major limitation for these cases is the size and speed of the computer available. Therefore, a move to the streaming array architecture can result in marked improvement in the data analysis techniques which may be employed.

Ioup, G. E.↗

Linking Transient Voltage to Spatially-Resolved Luminescence Imaging to Understand Reliability of Perovskite Photovoltaics

In this work, we present a methodology to separate effects of perovskite device metastability from irreversible degradation, using stress/rest cycling under constant current bias while collecting a series of electroluminescence images and continuously monitoring voltage. We develop a simulation model and procedures for image processing to better understand the effects of ion parameters on the transient nature of voltage and evolving electroluminescence images.

electroluminescence↗

Korean coastal water depth/sediment and land cover mapping (1:25,000) by computer analysis of LANDSAT imagery

Computer analysis was applied to single date LANDSAT MSS imagery of a sample coastal area near Seoul, Korea equivalent to a 1:50,000 topographic map. Supervised image processing yielded a test classification map from this sample image containing 12 classes: 5 water depth/sediment classes, 2 shoreline/tidal classes, and 5 coastal land cover classes at a scale of 1:25,000 and with a training set accuracy of 76%. Unsupervised image classification was applied to a subportion of the site analyzed and produced classification maps comparable in results in a spatial sense. The results of this test indicated that it is feasible to produce such quantitative maps for detailed study of dynamic coastal processes given a LANDSAT image data base at sufficiently frequent time intervals.

Park, K. Y.↗

GPU Accelerated Vector Median Filter

Noise reduction is an important step for most image processing tasks. For three channel color images, a widely used technique is vector median filter in which color values of pixels are treated as 3-component vectors. Vector median filters are computationally expensive; for a window size of n x n, each of the n(sup 2) vectors has to be compared with other n(sup 2) - 1 vectors in distances. General purpose computation on graphics processing units (GPUs) is the paradigm of utilizing high-performance many-core GPU architectures for computation tasks that are normally handled by CPUs. In this work. NVIDIA's Compute Unified Device Architecture (CUDA) paradigm is used to accelerate vector median filtering. which has to the best of our knowledge never been done before. The performance of GPU accelerated vector median filter is compared to that of the CPU and MPI-based versions for different image and window sizes, Initial findings of the study showed 100x improvement of performance of vector median filter implementation on GPUs over CPU implementations and further speed-up is expected after more extensive optimizations of the GPU algorithm .

Aras, Rifat↗

Applications of LIF to Document Natural Variability of Chlorophyll Content and Cu Uptake in Moss

Chlorophyll has long been used as a natural indicator of plant health and photosynthetic efficiency. Laser-induced fluorescence (LIF) is an emerging technique for understanding broad spectrum organic processes and has more recently been used to monitor chlorophyll response in plants. Previous work has focused on developing a LIF technique for imaging moss mats to identify metal contamination with the current focus shifting toward application to moss fronds and aiding sample collection for chemical analysis. Two laser systems (CoCoBi a Nd:YGa pulsed laser system and Chl-SL with two blue continuous semiconductor diodes) were used to collect images of moss fronds exposed to increasing levels of Cu (1, 10, and 100 nmol/cm 2 ) using a CMOS camera. The best methods for the preprocessing of images were conducted before the analysis of fluorescence signatures were compared to a control. The Chl-SL system performed better than the CoCoBi, with dynamic time warping (DTW) proving the most effective for image analysis. Manual thresholding to remove lower decimal code values improved the data distributions and proved whether using one or two fronds in an image was more advantageous. A higher DTW difference from the control correlated to lower chlorophyll a/b ratios and a higher metal content, indicating that LIF, with the aid of image processing, can be an effective technique for identifying Cu contamination shortly after an event.

59 BASIC BIOLOGICAL SCIENCES↗

SU-G-IeP3-11: On the Utility of Pixel Variance to Characterize Noise for Image Receptors of Digital Radiography Systems

Purpose: To characterize noise for image receptors of digital radiography systems based on pixel variance. Methods: Nine calibrated digital image receptors associated with nine new portable digital radiography systems (Carestream Health, Inc., Rochester, NY) were used in this study. For each image receptor, thirteen images were acquired with RQA5 beam conditions for input detector air kerma ranging from 0 to 110 µGy, and linearized ‘For Processing’ images were extracted. Mean pixel value (MPV), standard deviation (SD) and relative noise (SD/MPV) were obtained from each image using ROI sizes varying from 2.5×2.5 to 20×20 mm{sup 2}. Variance (SD{sup 2}) was plotted as a function of input detector air kerma and the coefficients of the quadratic fit were used to derive structured, quantum and electronic noise coefficients. Relative noise was also fitted as a function of input detector air kerma to identify noise sources. The fitting functions used least-squares approach. Results: The coefficient of variation values obtained using different ROI sizes was less than 1% for all the images. The structured, quantum and electronic coefficients obtained from the quadratic fit of variance (r>0.97) were 0.43±0.10, 3.95±0.27 and 2.89±0.74 (mean ± standard deviation), respectively, indicating that overall the quantum noise was the dominant noise source. However, for one system electronic noise coefficient (3.91) was greater than quantum noise coefficient (3.56) indicating electronic noise to be dominant. Using relative noise values, the power parameter of the fitting equation (|r|>0.93) showed a mean and standard deviation of 0.46±0.02. A 0.50 value for this power parameter indicates quantum noise to be the dominant noise source whereas values around 0.50 indicate presence of other noise sources. Conclusion: Characterizing noise from pixel variance assists in identifying contributions from various noise sources that, eventually, may affect image quality. This approach may be integrated during periodic quality assessments of digital image receptors.

60 APPLIED LIFE SCIENCES↗

Spin-wave based realization of optical computing primitives

We use micromagnetic simulations to demonstrate that spin waves can perform optically inspired, non-Boolean computing algorithms. We propose and design coherent spin-wave sources and phase shifters, which act akin to the key components of an optical signal processing system. We show that the functionality of the proposed on-chip spin-wave based signal processing system is similar to known optical computing devices. We argue that such computing system can serve as a practical, energy efficient, and integrated component of nanoscale image processing systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Enhanced Images for Checked and Carry-on Baggage and Cargo Screening

The current X-ray systems used by airport security personnel for the detection of contraband, and objects such as knives and guns that can impact the security of a flight, have limited effect because of the limited display quality of the X-ray images. Since the displayed images do not possess optimal contrast and sharpness, it is possible for the security personnel to miss potentially hazardous objects. This problem is also common to other disciplines such as medical X-rays, and can be mitigated, to a large extent, by the use of state-of-the-art image processing techniques to enhance the contrast and sharpness of the displayed image. The NASA Langley Research Centers Visual Information Processing Group has developed an image enhancement technology that has direct applications to this problem of inadequate display quality. Airport security X-ray imaging systems would benefit considerably by using this novel technology, making the task of the personnel who have to interpret the X-ray images considerably easier, faster, and more reliable. This improvement would translate into more accurate screening as well as minimizing the screening time delays to airline passengers. This technology, Retinex, has been optimized for consumer applications but has been applied to medical X-rays on a very preliminary basis. The resultant technology could be incorporated into a new breed of commercial x-ray imaging systems which would be transparent to the screener yet allow them to see subtle detail much more easily, reducing the amount of time needed for screening while greatly increasing the effectiveness of contraband detection and thus public safety.

Woodell, Glen↗

Neural Learning Based Blind Source Separation for Detection of Material Defects in Pulsed Thermography Images

In this paper, we introduce a neural learning-based approach to blind source separation for detection of material flaws in pulsed thermography (PT) images. This approach can be used to detect internal defects (pores) in metallic Additively Manufactured (AM) materials. Such defects occur in high-strength alloys produced with direct laser sintering AM method for nuclear energy applications. Pulsed thermal imaging system utilizes a high intensity flash lamp to rapidly heat surface of sample, a high sensitivity infrared camera to capture data of surface temperature variations. The data cube obtained with PT (stack of surface temperature images at different times) can be analyzed with image processing algorithms to detect material defects. Compared with conventional nondestructive evaluation (NDE) methods, such as digital radiography and ultrasonic testing, the PT pulsed infrared thermal detection technique has advantages of one-sided non-contact measurements, fast processing of large sample areas captured in one image. Detection of small material defects requires finding features in thermal images, which have signal contrast levels approaching sensitivity limit of IR camera. In this study, an optimized Neural Learning based Blind Source Separation (NLBSS) algorithm, including Principal Component Analysis (PCA), and Independent Component Analysis (ICA) is demonstrated to automatically extract principal temporal and spatial features of thermography frames to enhance flaw detection. By using the NLBSS algorithm, material internal defects can be automatically detected. Furthermore, this processing approach compensates for experimental thermal imaging artifacts, such as noise and uneven heating. By merging artificial intelligence with the photothermic, the NDE system detects internal calibrated defects of various sizes and depths in AM nuclear-grade metallic alloys.

Zhang, Xin↗

Covisualization by computational optical-sectioning microscopy of integrin and associated proteins at the cell membrane of living onion protoplasts

Using higher-resolution wide-field computational optical-sectioning fluorescence microscopy, the distribution of antigens recognized by antibodies against animal beta 1 integrin, fibronectin, and vitronectin has been visualized at the outer surface of enzymatically protoplasted onion epidermis cells and in depectinated cell wall fragments. On the protoplast all three antigens are colocalized in an array of small spots, as seen in raw images, in Gaussian filtered images, and in images restored by two different algorithms. Fibronectin and vitronectin but not beta 1 integrin antigenicities colocalize as puncta in comparably prepared and processed images of the wall fragments. Several control visualizations suggest considerable specifity of antibody recognition. Affinity purification of onion cell extract with the same anti-integrin used for visualization has yielded protein that separates in SDS-PAGE into two bands of about 105-110 and 115-125 kDa. These bands are again recognized by the visualization antibody, which was raised against the extracellular domain of chicken beta 1 integrin, and are also recognized by an antibody against the intracellular domain of chicken beta 1 integrin. Because beta 1 integrin is a key protein in numerous animal adhesion sites, it appears that the punctate distribution of this protein in the cell membranes of onion epidermis represents the adhesion sites long known to occur in cells of this tissue. Because vitronectin and fibronection are matrix proteins that bind to integrin in animals, the punctate occurrence of antigenically similar proteins both in the wall (matrix) and on enzymatically prepared protoplasts reinforces the concept that onion cells have adhesion sites with some similarity to certain kinds of adhesion sites in animals.

NASA Discipline Plant Biology↗

SU-E-T-04: 3D Dose Based Patient Compensator QA Procedure for Proton Radiotherapy

Purpose: In proton double-scattering radiotherapy, compensators are the essential patient specific devices to contour the distal dose distribution to the tumor target. Traditional compensator QA is limited to checking the drilled surface profiles against the plan. In our work, a compensator QA process was established that assess the entire compensator including its internal structure for patient 3D dose verification. Methods: The fabricated patient compensators were CT scanned. Through mathematical image processing and geometric transformations, the CT images of the proton compensator were combined with the patient simulation CT images into a new series of CT images, in which the imaged compensator is placed at the planned location along the corresponding beam line. The new CT images were input into the Eclipse treatment planning system. The original plan was calculated to the combined CT image series without the plan compensator. The newly computed patient 3D dose from the combined patientcompensator images was verified against the original plan dose. Test plans include the compensators with defects intentionally created inside the fabricated compensators. Results: The calculated 3D dose with the combined compensator and patient CT images reflects the impact of the fabricated compensator to the patient. For the test cases in which no defects were created, the dose distributions were in agreement between our method and the corresponding original plans. For the compensator with the defects, the purposely changed material and a purposely created internal defect were successfully detected while not possible with just the traditional compensator profiles detection methods. Conclusion: We present here a 3D dose verification process to qualify the fabricated proton double-scattering compensator. Such compensator detection process assesses the patient 3D impact of the fabricated compensator surface profile as well as the compensator internal material and structure changes. This research receives funding support from CURA Medical Technologies.

60 APPLIED LIFE SCIENCES↗