Opening Files in CyteSeer
CyteSeer's scalable design is evident in how it works with files. CyteSeer doesn't "open" files in the traditional sense. It looks for files of a certain format, analyses those files and saves the results in a set of new files. The original files are never modified in CyteSeer, only the result files for image masks and numeric data.
CyteSeer works with many image file formats
CyteSeer is built to open and use files from a growing number of high-content analysis instruments and digital microscopes. CyteSeer can analyze bmp, tif, png, gif & jpg from any system. CyteSeer will generally select the correct file type automatically. The remainder of this document offers more detail.
Point to the Plate Directory
When browsing for files in CyteSeer, select the plate level directory. This can vary from format to format because the conventions vary from device to device. As shown above, the Generic, Free Form Gray Images & Free Form RGB Images formats all expect the all of the images to be in the top level of the selected directory.
Formats vary from device to device
Many other formats, including but not limited to the IC 100, Opera, GE InCell images have a well defined structure for where the images are stored for each plate. CyteSeer knows about these formats. Simply browse to the top level plate directory for all the files.
Working with Images of Arbitrary Type
CyteSeer supports viewing almost any type of image via the Free-Form RGB Images and Free-Form Gray Images formats. Free-form refers to the arbitrary naming of the files. As a major advantage of an automated cell image analysis tool is the ability to analyze many images – often 1,000's of images – at one time, an arbitrary free-form naming scheme has limited value because it is difficult to parse and track the results. That said, testing analysis settings and resulting masks during assay development can be very useful.
Free Form RGB Images:
This naming option supports bmp, tif, gif and jpg files of any name. The option assumes the images are standard, three color images that might come from a merged pseudo-color microscope software or screenshot.
Free Form Gray Images:
This naming option support bmp, tif, gif and jpg files of any name. The option assumes the images are single color gray scale images that might be saved directly from a digital microscope. The option requires matching the channel – i.e. channel 0 – with the channel name – i.e. Nucleus.
Working with Batches of Many Plates
CyteSeer can analyze batches of many plates within a single run.
1) Select "Batch" to the right of the Image Naming Convention drop-down menu.
2) Select a directory with many plate directories to be processed. CyteSeer can only process one type of plate and one set of algorithm conditions at one time.
3) If the Run button is highlighted and a set of plates are ready selected to be analyzed, CyteSeer will analyze the entire batch.
Supporting New Formats
We are always looking to support new formats in CyteSeer. Please contact us directly to request new formats to support.
Vala Sciences Contact Information
Vala Sciences is a cell biology company offering software, kits, services and custom development for analyzing a wide variety of cell types and conditions from adipocytes & stem cells to primary & well established cell lines.
Vala Sciences Inc. | Sales and technical information:
858.461.6861 | support@valasciences.com | http://valasciences.com
Links: | CyteSeer free download and trial | Kit ordering Information | Forum | Tutorials | Application Notes
Services: HCS Screening Services, IC 100 Warranty Service and Hardware Upgrades
