Raw data related to near-field ptychographic X-ray computed tomography (nf-PXCT) dataset of a resin-embedded, heavy metal stained brain specimen of about 100 micron diameter acquired at the cSAXS beamline in 2020. The different datasets are: documentation: includes the logbook describing the experimental procedures, and some information about the sample, which is called EPL-4. Measurement was performed using the OMNY instrument at cryogenic temperature. cxs_software: the cSAXS software in Matlab, including PtychoShelves for ptychographic reconstructions and scripts for tomographic reconstruction. These scripts were used during the experiment to process the data online, performing both ptychographic and tomographic reconstructions, which will be published separately as derived data. S28-1543_ID2: motor positions and detector frames corresponding to the ptcychographic scans of all projections