As I stated at the start of the last episode both Niccolò Leoniceno (1428–1524) and Pandolfo Collenuccio (1444–1504), in their dispute over the quality, or lack of it, of Pliny’s Historia Naturalis, saw the need to go beyond comparing the description of plants in Pliny with those in the works of Theophrastus and Dioscorides and actually go out into nature and look at real plants. This empirical turn was the start of something new within the intellectual culture of medieval Europe and would eventually lead to the establishment of botany as an independent scientific discipline.
As Collenuccio wrote in his Pliniana defensio in 1493,
[The researcher] ought to ask questions of rustics and mountaineers, closely examine the plants themselves, note the distinction between one plant and another; and if need be he should even incur danger in testing the properties of them and ascertaining their remedial value.
and this is exactly what they began to do. Although they all contained information on plants from other parts of the world, India for example, the works of Pliny, Theophrastus, and Dioscorides were all predominantly based on the flora of the Mediterranean, so it was comparatively easy for those professors of medicine in the Northern Italian universities to actually undertake empirical surveys of the local plant life and compare it with the information contained in the works of the botanical authorities from antiquity.
Since antiquity, apothecaries and herbalists had been going out into nature to search for and harvest herbs for their work. However, the scholars from the university were now going out for the first time and with a different aim. On their excursions, they were looking for herbs to describe, to study them and bring specimens back to both study in depth and to show to students in their materia medica courses. Leoniceno and his students Euricus Cordus (1486–1535) and Antonio Musa Brasavola (1500–1555) led the way in this new activity for scholars, with Cordus and Brasavola publishing guides to collecting. The former his Botanologicon (1535) and the latter Examen omnium simplicium medicamentorum, quorum in officinis usus est (1537).
The next development was not just to bring back specimens to display to students during their courses but to take the students out with them on the botanising excursions, and so the field trip was born. The first professor of simples at both Bologna and Pisa, Luca Ghini (1490–1556) initiated the field trip.
As with the spread of the materia medica lectures at the North Italian universities, the field trip quickly spread to universities throughout Europe by 1540. Guillaume Rondelet (1507–1666) in Montpellier was particularly renowned for his field trips, influencing a whole generation of future influential physicians.
The next development in the empirical study of simples was instead of taking the students into the countryside to search for and study the herbs in their natural habitat, to bring the living specimens to the universities in the form of the botanical garden.
Herbal gardens for growing medicinal herbs were not a new invention in the Renaissance they had existed in one form or another since antiquity. There is some evidence that Aristotle and/or Theophrastus established a physic garden in the Lyceum at Athens but to what extent it was similar to the highly organised Renaissance botanical gardens is disputed. Pliny relates that the Roman botanist and pharmacologist, Antonius Castor (1stcentury CE) cultivated a large botanical garden. Gardens in general declined with the Roman Empire but during the Carolingian Renaissance gardens became an important feature of European monasteries. As well as gardens for fruit and vegetables, which the monks grew from their own nourishment, these featured section for the cultivation of medical herbs known as the herbularis or hortus medicus and more general as physic gardens.
The typical cloister garden was a square or rectangular plot divided into quadrants by paths. The centre, where the paths intersected was often occupied by a well, which provided water for the monastery as well as for the garden itself.
As medieval aristocrats began to create pleasure gardens on their estates in the High and Late Middle Ages these were mostly modelled on the monastery gardens.
By the early sixteenth century private gardens were quite common.
As it was often impossible to create gardens in the densely built inner towns and cities, the gardens were often outside of the city walls. In 1334, Matthaeus Silvaticus (c. 1280–c. 1342), the author of notable pharmacopoeia, Pandectarum Medicinae, established a botanical garden in Salerno in Southern Italy, home of the Schola Medica Salernitana. In 1447, Pope Nicholas V (1397–1455), who had facilitated the acquisition of the botanical works of Theophrastus and their translation into Latin, set aside part of the Vatican grounds for a garden of medicinal plants that were used to promote the teaching of botany.
On 29 June of 1545, the Republic of Venice authorised the foundation of a botanical garden at the University of Padua so that “scholars and other gentlemen can come to the gardens at all hours in the summer, retiring in the shade with their books to discuss plants learnedly, and investigating their nature peripatetically while walking”
We can see in this quote that like the libraries, which were being established around the same time, that the gardens were conceived as places were scholars could exchange and discuss their academic views.
A month later, in July, The Grand Duke of Tuscany, Cosimo I, concluded negotiations for a garden at the University of Pisa, founding another at the convent of San Marco in Florence in December. The university botanical garden was under the leadership of Luca Ghini (1490–1556) the professor for medical simples.
As with other development in the establishment of materia medica at the universities Florence followed suit in 1545, Pavia in 1558, and Bologna in 1568. In Spain, the royal physician pharmacologist, and botanist, Andrés Laguna (1499–1559), used the Italian example to persuade Philip II to fund a royal physic garden at Aranjuez, as he wrote in his translation of Dioscorides’ De materia medica in 1555.
All the princes and universities of Italy take pride in having excellent gardens, adorned with all kinds of plants found throughout the world, and so it is most proper that Your Majesty provide and order that we have at least one in Spain, sustained with royal stipends.
His appeal was successful. The concept of a university botanical garden spread throughout Europe, Valencia in 1567, Kassel 1568, Leiden 1587, Leipzig 1580, Basel 1589, and Montpellier 1593. In the seventeenth century the concept spread into Northern Europe and Britain.
The botanical gardens were created with plants from all over the world, this meant the necessity to acquire plants and seeds from other areas by some means or another. We shall address this aspect of the development of botany in a future episode. A final aspect of the development of the botanical gardens was that they were not simply collection of living plants to be studied by students, so that they could learn to recognise the ingredients of the medicines they would be prescribing but they became centres of botanical and medical research. Rooms containing distilleries and other apparatus that could be used as laboratories were built around the gardens to enable scientific research to be carried out on the plants grown there. Along with the anatomical theatres and libraries the botanical gardens became part of an increasing research apparatus on the Renaissance universities.
The Renaissance Mathematicus 
You’ve left out Ullise Aldrovandi, although you mentioned the date and place, who, despite his atrocious sense of taxonomy, is reputed to have created the first public botanic garden at the University of Bologna in 1568. I do not know if Ghini’s competed with his. Many commentators believe Aldrovandi’s was the first really complete garden.
I’m immensely impressed with this series, and the only reason I haven’t commented is that I haven’t detected any mistakes. This site is becoming the Encyclopédie of the Age, which is especially amazing when you realize that Diderot had a lot of help.