We investigated the effect of short-term teaching (3 weeks) using image analysis on gymnasium/secondary school students' (ISCED3A) skills (science process skills, SPS) and knowledge using Fiji (ImageJ) software. The theoretical teaching was combined with IT-based education (measurement of the area or signal intensity on photos from scientific papers using algae "Ulva" or "Coccomyxa" and the fungus "Glomerella") and students formed conclusions from data and answered knowledge questions. Experimental education increased score (post-test/pre-test) in the area of knowledge (by 102%) and SPS (by 44%) and greater impact of IT implementation on the development of girls' SPS and knowledge was found. Besides, the Pearson's correlation analysis showed a more intense improvement of students who had greater deficiencies in pre-test. This experimental gymnasium group (n = 53) also retained a higher score in re-test in comparison with control gymnasium students (without the implementation of image analysis, n = 54) and detailed analysis of individual questions revealed that there was a development of SPS, especially those that were emphasized in the experimental teaching. Another control group "university students" (ISCED5A, n = 19) had a higher score in re-test than the experimental gymnasium group, but the area of knowledge was comparable. These results indicate that the involvement of IT improves SPS and knowledge of gymnasium students at the level comparable with university students. The test and worksheets are attached for free use with the aim of improving the teaching of less interesting topics such as botany.