MicroFile+ Free Software for Converting Big Scientific Images into Manageable, Shareable, Standardized Files
For Immediate Release: Williston, VT — October 6, 2020 — Big science produces big data. At laboratories around the world, researchers
MicroFile+
Makes it easy to view, analyze, and share big image data from many sourcesProduct Overview
MicroFile+ is a free tool that solves a problem faced across laboratories and imaging facilities. Modern microscopic imaging devices can generate vast quantities and types of data. Organizing, storing, and analyzing this big data is a daunting problem that MicroFile+ solves. MicroFile+ turns large, unwieldy multi-dimensional data from most imaging sources into compact, easy to manage, and documented files that can be instantly loaded by MBF Bioscience products for analyses. The files can also be used by numerous other software applications. MicroFile+ also preserves instrumental and experimental metadata and includes extensive functionality for adding and curating metadata to fully describe and document image data.
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Key Benefits
- Convert nearly any type of image to the jpeg2000 standard or to the OME tiff format
- Compresses files for efficient storage and web streaming
- Easily add and edit metadata pertaining to your files
- Efficiently and accurately convert 2D and 3D images from almost any source and format into manageable, standardized file formats
- Compile individual images, such as serial sections or cleared tissue, into 3D volumes
- Optimized to work with multi-terabyte 3D images from lightsheet microscopes
MicroFile+ uses state-of-the-art compression methods to efficiently and accurately convert 2D and 3D images from most sources and formats into manageable, standardized experimental results. Formats from slide scanners, confocal microscopes, light sheet microscopes, and standard sources are all supported. Convert nearly any type of image to the widely used jpeg2000 or OME-TIFF standards. These formats efficiently store big image and metadata for fast retrieval, viewing, and analyses across applications. MicroFile+ can convert images without limits on the number of fluorescent and brightfield channels in the experiment.
MicroFile+ was developed with support by the SPARC program [Grant number 3OT3OD025349-01S2]
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Download MicroFile+ product sheet here.
MicroFile+® Version 2021
Released 2021
New Features and Enhancements:
- Convert image data into two standard formats:
- jpeg2000
- OME tiff
- Easily add and edit metadata pertaining to your files
- Efficiently and accurately convert 2D and 3D images from almost any source and format into manageable, standardized file formats
- Convert data from slide scanners, confocal microscopes, light sheet microscopes, and standard sources
- Convert fluorescence images with no limits on the number of fluorescence and bright field channels in the experiment
- MicroFile+ software uses multi-threading to optimally utilize computer resources ranging from standard Windows computers to advanced multi-core workstations
- Compatible input file formats include:
- JPEG2000 (.jp2)
- JPEG (.jpg)
- TIFF (.tif)
- Generic TIFF
- Vesalius TIFF
- Flowview TIFF (Olympus)
- OME TIFF
- Keyence TIFF
- Imaris TIFF
- Zeiss CZI (.czi)
- Leica LIF (.lif)
- LSM
- SVS/Huron
- CaliberID
- OIB/OIF
- Imaris IMS
- ND2
- NDPI
View Full Version History Here.
MicroFile+: Key Features
Direct Conversion
Convert nearly any type of image to the jpeg2000 or OME-TIFF standards. These formats efficiently store big image and metadata for fast retrieval, viewing, and analyses across applications. MicroFile+ supports: MBF JPEG2000, JPEG, generic TIFF, Vesalius/CaliberID TIFF, Flowview Olympus TIFF, OME TIFF, Keyence TIFF, Imaris TIFF, Zeiss LSM, Huron SVS, Leica SVS, CaliberID, HDF5, Imaris IMS, NDPI, DICOM, ND2, and LIF.
MicroFile+: Key Features
Combine 2D images into a 3D stack
Compile individual 2D images, such as serial sections or cleared tissue images, into 3D volumes.
MicroFile+: Key Features
Multichannel Conversion
MicroFile+ can handle complex data formats generated by lightsheet and fast scanning imaging platforms. Nearly any image format can be consolidated into accessible and understandable organization.
MicroFile+: Key Features
Combine images into a projection image
Produce popular data visualizations from series of images including deep focus, and maximum and minimum intensity projections on big data sets.
Who Is Using MicroFile+?
Microfile+ is used across the globe by the most prestigious laboratories.
News About MicroFile+
MBF Bioscience Releases our File Format to Embrace FAIR Data Standards
For Immediate Release: Williston, VT (September 25, 2020)—To support the scientific community’s movement toward a more open and collaborative climate, MBF
Cited in Peer Reviewed Scientific Publications
MBF’s software utility is underscored by the number of references it receives in the worlds most important scientific publications.
Ament, S. A., M. Cortes-Gutierrez, et al.
A single-cell genomic atlas for maturation of the human cerebellum during early childhoodView Publication
Timonidis, N., M. Rubio-Teves, et al.
Analyzing Thalamocortical Tract-Tracing Experiments in a Common Reference SpaceView Publication
Jeon, K.-I., A. Kumar, et al.
Blocking Mitochondrial Pyruvate Transport Alters Corneal Myofibroblast Phenotype: A New Target for Treating FibrosisView Publication
Tetsushi, N., F. Satoshi, et al.
Microglia are dispensable for developmental dendrite pruning of mitral cells in miceView Publication
Qin, Y., X.-Y. Zhang, et al.
Downregulation of mGluR1-mediated signaling underlying autistic-like core symptoms in Shank1 P1812L-knock-in miceView Publication
Nevue, A. A., B. M. Zemel, et al.
Cell type specializations of the vocal-motor cortex in songbirdsView Publication
Frequently Asked Questions (FAQ)
What does this converter do?
The MicroFile+ converter identifies any recognizable metadata associated with files to pre-populate metadata fields. This minimizes the information that you need to input for converting image(s) to different image format(s). To obtain converted files that contain as much metadata as possible, we recommend that you convert files created using the default image-acquisition format for your imaging system.
What compression level is appropriate for my image data?
The appropriate compression level must be determined empirically. We suggest that you start testing with a 40:1 compression ratio. Open the images in your analysis software and compare with images that are not compressed. If there are visible artifacts, convert the source image again with a 20:1 compression ratio and compare to uncompressed image files. Repeat as needed, halving the compression ratio until there are no visible artifacts compared to uncompressed images.
We invite you to our forum for MicroFile+ software, where you can message experts and other users about topics like compression and other MBF Bioscience products.
Can deconvolved images be converted?
Any image in a compatible format can be converted. See specification section above for compatible file formats.
Is the data generated with MicroFile+ FAIR?
Yes. MicroFile+ supports the collaborative goals of Open Science through the practice of data openness, integrity, and reproducibility, by using MBF Bioscience’s published digital reconstruction data file format, the Neuromorphological File Specification (NFS), which was recently endorsed by the INCF. The data elements in this NFS format were specifically implemented to ensure the files are Findable, Accessible, Interoperable, and Reusable (FAIR).
Testimonials
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"MBF provides excellent technical support and helps you to find the best technical tools for your research challenges on morphometry."
Robust Professional Support
Our service sets us apart, with a team that includes Ph.D. neuroscientists, experts in microscopy, stereology, neuron reconstruction, and image processing. We’ve also developed a host of additional support services, including:
- Forums
We have over 25 active forums where open discussions take place.
>> Learn More - On-Site/Training
We’ve conducted over 750 remote software installations.
>> Learn More - Webinars
We’ve created over 55 webinars that demonstrate our products & their uses.
>> Learn More
Download MicroFile+
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