Live cell visualization and analysis
Systems and methods are provided for automatically imaging and analyzing cell samples in an incubator. An actuated microscope operates to generate images of samples within wells of a sample container across days, weeks, or months. A plurality of images is generated for each scan of a particular well, and the images within such a scan are used to image and analysis metabolically active cells in the well. Tins analysis includes generating a “range image” by subtracting the minimum intensity value, across the scan, for each pixel from the maximum intensity value. This range image thus emphasizes cells or portions of cells that exhibit changes in activity over a scan period (e.g., neurons, myocytes, cardiomyocytes) while de-emphasizing regions that exhibit consistently high intensities when images (e.g., regions exhibiting a great deal of autofluorescence unrelated to cell activity).
1. A method of imaging and analyzing cell samples in a cell culture vessel, the method comprising:
capturing a movie of the cell culture vessel;
generating a static range image from the movie, wherein the static range image is composed of pixels representing the minimum fluorescence intensity subtracted from the maximum fluorescence intensity at each pixel location over a complete scan period; and
defining objects by segmenting the static range image.
2. The method of claim 1 , further comprising:
from the objects, deriving average object mean intensities from the complete scan period.
3. The method of claim 1 , further comprising:
from the objects, deriving a pairwise correlation analysis of all object traces over the complete scan period.
4. The method of claim 1 , further comprising:
from the objects, deriving a mean of all objects mean burst duration from the complete scan period.
5. The method of claim 1 , further comprising:
from the objects, deriving a strength of each burst of all objects from the complete scan period.
6. The method of claim 5 , further comprising:
deriving an overall burst strength metric as a mean of all objects mean burst strength from the complete scan period.
7. The method of claim 1 , further comprising:
from the objects, deriving a mean of all objects burst rate from the complete scan period.
8. The method of claim 1 , wherein segmenting the range image is completed by optimizing one or more of a background subtraction, defining the minimum cell width, and a fluorescence thresholding.
9. The method of claim 1 , wherein the objects are defined as one or more of a neuron, a dendrite, an axon and a synapse.
10. The method of claim 1 , further comprising:
determining a number of active objects defined by a total number of segmented objected detected within the complete scan period.
11. The method of claim 1 , further comprising:
storing, in a database, one or more metrics derived from the objects.
12. The method of claim 1 , wherein the complete scan period occurs every 24 hours.
13. The method of claim 1 , wherein the complete scan period comprises a three minute scan period.
14. The method of claim 1 , wherein the movie of the cell culture vessel comprises a set of images taken at a rate of three images per second over the complete scan period.
15. The method of claim 1 , wherein the cell culture vessel comprises a microplate including a plurality of sample wells.
16. A non-transitory computer-readable medium, configured to store at least computer-readable instructions that, when executed by one or more processors of a computing device, cause the computing device to perform computer operations carrying out the method of claim 1 .
17. A system comprising:
one or more processors; and
a non-transitory computer-readable medium, configured to store at least computer-readable instructions that, when executed by the one or more processors, cause the system to perform the method of claim 1 .
18. A method of imaging and analyzing cell samples in a cell culture vessel, the method comprising:
capturing a movie of the cell culture vessel, wherein the cell culture vessel comprises a microplate including a plurality of sample wells; and
generating a static range image from the movie, wherein the static range image is composed of pixels representing the minimum fluorescence intensity subtracted from the maximum fluorescence intensity at each pixel location over a complete scan period.
19. The method of claim 18 , wherein the complete scan period occurs every 24 hours.
20. The method of claim 18 , wherein the complete scan period comprises a three minute scan period.
21. The method of claim 18 , wherein the movie of the cell culture vessel comprises a set of images taken at a rate of three images per second over the complete scan period.
22. A non-transitory computer-readable medium, configured to store at least computer-readable instructions that, when executed by one or more processors of a computing device, cause the computing device to perform computer operations carrying out the method of claim 18 .
23. A system comprising:
one or more processors; and
a non-transitory computer-readable medium, configured to store at least computer-readable instructions that, when executed by the one or more processors, cause the system to perform the method of claim 18 .