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An apparatus includes a housing, a reaction vial and a transfer mechanism. The housing defines a first flow path and a second flow path. The housing has transfer port defining an opening in fluid communication with the second flow path and a volume outside of the housing. The transfer port includes

An apparatus includes a housing, a reaction vial and a transfer mechanism. The housing defines a first flow path and a second flow path. The housing has transfer port defining an opening in fluid communication with the second flow path and a volume outside of the housing. The transfer port includes a flow control member to limit flow through the opening. The reaction vial is coupled to the housing and defines a reaction volume, which is in fluid communication with the transfer port via the second flow path. The transfer mechanism is configured to transfer a sample from an isolation chamber of an isolation module to the reaction chamber via at least the first flow path when the transfer mechanism is actuated. The transfer mechanism configured to produce a vacuum in the reaction vial to produce a flow of a sample from the isolation chamber to the reaction volume.

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1. An apparatus, comprising: a housing defining a first flow path and a second flow path, the housing having a flow cell portion defining a detection volume, wherein the flow cell portion is located within an extension of the housing;a reaction vial coupled to the housing, the reaction vial defining

1. An apparatus, comprising: a housing defining a first flow path and a second flow path, the housing having a flow cell portion defining a detection volume, wherein the flow cell portion is located within an extension of the housing;a reaction vial coupled to the housing, the reaction vial defining a reaction volume, the reaction volume in fluid communication with the detection volume via the first flow path; anda transfer mechanism in fluid communication with the detection volume via the second flow path, the transfer mechanism configured to transfer a sample from the reaction volume to the detection volume when the transfer mechanism is actuated;an optics module interfaced with the extension, wherein: the apparatus is configured to allow the sample to flow within the first flow path in a first direction into the detection volume while a second portion of the sample flows within the second flow path in a second direction opposite the first direction;the optics module comprises a magnet. 2. The apparatus of claim 1, wherein: the sample includes a plurality of particles within a fluid; and the flow cell portion includes a flow structure configured to control the passage of the plurality of particles through the detection volume. 3. The apparatus of claim 1, wherein the transfer mechanism is configured to produce a vacuum in the detection volume to produce a flow of the sample from the reaction volume to the detection volume. 4. The apparatus of claim 1, wherein a wall defining at least a portion of the boundary of the detection volume is constructed of a compliant material. 5. The apparatus of claim 1, wherein a wall of the flow cell portion is configured to move when the sample is transferred from the reaction volume to the detection volume. 6. The apparatus of claim 1, wherein the flow cell portion includes a valve configured to selectively fluidically isolate the reaction volume from the detection volume. 7. The apparatus of claim 1 wherein the transfer mechanism comprises a plunger. 8. The apparatus of claim 7 wherein the plunger is configured to produce a vacuum within the detection volume. 9. The apparatus of claim 7 wherein the plunger is configured to open a volume within the transfer mechanism within which a portion of the sample can flow after passing through the flow cell portion. 10. The apparatus of claim 1 wherein the optics module comprises a light source. 11. The apparatus of claim 10 wherein the light source is a light emitting diode (LED). 12. The apparatus of claim 1 wherein the optics module comprises multiple light sources configured to emit different wavelengths of light. 13. The apparatus of claim 1 wherein the optics module comprises a light detector. 14. The apparatus of claim 13 wherein the light detector is a CCD camera. 15. The apparatus of claim 1 wherein the flow cell portion comprises a flow structure configured to control the passage of the sample through the detection volume.