Here are the questions I asked Irina and her responses:

Q1 Why do my clots look like spider webs rather than ropes? (Show Irina my images, 3D prints and a dummy slide.)

A1 Nail polish absorbs water. My samples could be dessicated. Use silicon grease instead, and only apply it to the open sides, i.e. the top and bottom. The sides on double-sided tape are already sealed.

Q2 Should clots be isotropic (in vivo and in vitro)? My fibrils look thicker along the z-axis.

A2 Real clots in human bodies should be isotropic. Irina thinks the most likely possibility is that despite the high vertical resolution I use, there is still some smearing in the z-direction inherent to the optics. Software could also play a part—Irina uses Volocity, which she says is expensive. Carr maintains that the geometry (in particular the small z-height) of the slide chamber and the negative charge of glass could play a role, though Irina thinks away from the boundaries these should have little impact on clot structure.

Q3 (Why) is dialysis of fibrinogen with NaCl-Tris buffer really necessary? How can fibrinogen be protected from heat?

A3 Dialysis is necessary because the buffer in the stock may not be correct. Irina dialyses at 4°C rather than room temperature, overnight. This could also relate to Q1.

Q4 What is the physiological range of clot densities in the human body, i.e. are my sample images representative of clinical conditions?

A4 In a human body there is much more variation, even in a single thrombus. For instance in the vicinity of a platelet the concentration of thrombin may be higher than it is farther away. Fibrin therefore forms bundles. Real thrombi do not have the homogeneity of my samples.