FLUIDIC DEVICES WITH BEAD WELL GEOMETRIES WITH SPATIALLY SEPARATED BEAD RETENTION AND SIGNAL DETECTION SEGMENTS AND RELATED METHODS

1 . An analysis system comprising:

a controller;

an image processor;

a detector in communication with the image processor;

a microfluidic device comprising a plurality of reaction wells, each comprising a single bead retention segment and at least one signal detection segment in fluid communication with and spatially separated from the single bead retention segment,

(i) wherein the at least one signal detection segment comprises an elongate channel that extends along a length direction and has a width that extends in a direction perpendicular to the length direction that is less than a width of an adjacent single bead retention segment and less than a diameter of a single bead,

(ii) wherein centerlines of single bead retention segments of neighboring reaction wells are spaced apart a distance of between 1 μm and 1 mm,

(iii) wherein at least one of the at least one signal detection segment has an end portion that resides a distance of between 0.3× to 200× of a diameter of a single bead, from one or more of the single bead retention segments,

(iv) wherein the width of the elongate channel is 25%-75% less than the width of the adjacent single bead retention segment,

(v) wherein the reaction wells are provided in a density in a range of about 6,000 wells/cm 2 to about 2,000,000 wells/cm 2 ,

(vi) wherein each of the plurality of reaction wells has a volumetric capacity in a range of 1 aL to 1 μL, and

(vii) wherein the microfluidic device comprises a sealing agent that seals the reaction wells from each other such that the plurality of reaction wells are in fluid isolation from each other;

and

a plurality of single beads, wherein the single beads are magnetic beads,

wherein the image processor is configured to identify parallel and spaced apart optical signals corresponding to different respective signal detection segments of the plurality of reaction wells of the microfluidic device while the single beads are held in the corresponding single bead retention segments; and

wherein the optical signals are optically distinguishable from background signals of the single beads held in the corresponding single bead retention segments.

2 . The system of claim 1 , wherein the single bead retention segments have a geometry configured to restrict the loading of the single beads to one or zero beads per single bead retention segment.

3 . The system of claim 1 , wherein the plurality of reaction wells have a common size.

4 . The system of claim 1 , wherein in the plurality of reaction wells, at least one reaction well has a different size from at least another one.

5 . The system of claim 1 , wherein the single bead retention segment and the at least one signal detection segment of each of the plurality of reaction wells comprise tapered and/or straight walls formed into a planar substrate of the microfluidic device.

6 . The system of claim 1 , wherein the plurality of single beads comprise reagents and/or analytes comprising a cleavable bond, and wherein the reagents and/or analytes are capable of being released from the single beads into the reaction wells.

7 . The system of claim 6 , wherein the reagents and/or analytes released from single beads held in the single bead retention segments diffuse through a common solution volume of the reaction wells.

8 . The system of claim 1 , wherein the optical signals comprise fluorescence signals.

9 . The system of claim 1 , wherein the plurality of single beads are provided as different types of single beads, and wherein one or more of the reaction wells comprise a different type of single bead from one or more other ones of the reaction wells.

10 . The system of claim 9 , wherein each different type of single bead is encoded with a unique signature and each different type of single bead is functionalized with a different reagent.

11 . The system of claim 10 , wherein the image processor is configured to detect the optical signals for the plurality of reaction wells, and the image processor is configured to detect different analytes and/or different chemical reactions as the detected optical signals.

12 . The system of claim 1 , wherein the microfluidic device is a microfluidic chip.

13 . The system of claim 1 , wherein the single bead retention segment and the at least one signal detection segment reside in a first planar substrate with the first planar substrate defining an open upper surface and sidewalls of the single bead retention segment and the at least one signal detection segment, and wherein the microfluidic device further comprises a second planar substrate that couples to the first planar substrate and defines a closed outer surface with at least one fluid port.

14 . The system of claim 1 , wherein the plurality of reaction wells are formed between an upper substrate and a lower substrate.

15 . The system of claim 1 , wherein the single bead retention segment is sized and configured to hold a single bead with a diameter in a range of 100 nm to 1 mm, and wherein a width of the single bead retention segment is in a range of 101% to 195% of the diameter of a respective single bead held therein.

16 . The system of claim 1 , wherein the image processor is configured to identify the optical signals present in the at least one signal detection segment of the reaction wells after a reaction without requiring a baseline readout from the detector before the reaction.

17 . The system of claim 1 , wherein the image processor is configured to identify whether the optical signals are positive assay signals.

18 . The system of claim 17 , wherein the image processor is configured to carry out bead decoding in the reaction wells with one or more identified positive assay signals before or during when an assay is carried out.