Photon-based (bosonic-type) imaging at short wavelength vs. electron, or recently neutron, imaging has additional advantages due to different interaction of photons with matter and thus high resolution photon-based imaging is still of high interest to the scientific community. In this work we try to combine the advantages of employing compact, laboratory type laser-plasma short wavelength source, based on Ar/He gas puff target, emitting incoherent radiation, with the “water-window” spectral range. This unique combination is highly suitable for biological imaging, and allows developing a small size microscopy setup, which might be used in various fields of science and technology. Thus, in this paper we report on recent advances in “water-window” desk-top microscopy setup employing a laser-plasma SXR source based on a double stream gas puff target and Wolter type-I objective. The system allows capturing magnified images of the objects with ~1 μm spatial resolution up to ~40 μm thickness and single SXR pulse exposure time as low as 3 ns. For the SXR microscope Ar plasma was produced by focusing of the pumping laser pulses, from Nd:YAG laser (Eksma), by a lens onto a gas puff target. EUV radiation from the plasma was collected and focused by an ellipsoidal, axi-symmetrical nickel coated condenser mirror, developed by Rigaku, Inc. The condenser is a broad-band optic, capable of efficiently reflecting radiation from the EUV range down to SXR region with energy cut-off of ~800 eV. To spectrally narrow the emission from argon plasma a free-standing titanium filter (Lebow) was used. Spectrally filtered radiation illuminates the sample. Then the sample was imaged onto a SXR sensitive back-illuminated, CCD camera (Andor) by a Wolter type-I reflective objective. A characterization and optimization of both the source and the microscope setups are presented and discussed.